diff --git a/qiime/format.py b/qiime/format.py
index 9789479ecd..60332350e3 100755
--- a/qiime/format.py
+++ b/qiime/format.py
@@ -3,7 +3,8 @@
 __author__ = "Rob Knight"
 __copyright__ = "Copyright 2011, The QIIME Project"
 __credits__ = ["Rob Knight", "Justin Kuczynski", "Jeremy Widmann",
-               "Antonio Gonzalez Pena", "Daniel McDonald", "Jai Ram Rideout"]
+               "Antonio Gonzalez Pena", "Daniel McDonald", "Jai Ram Rideout",
+               "Mike Robeson"]
 # remember to add yourself if you make changes
 __license__ = "GPL"
 __version__ = "1.8.0-dev"
@@ -14,13 +15,14 @@
 from numpy import asarray, isnan, log10, median
 from StringIO import StringIO
 from re import compile, sub
-from os import walk
+from os import walk, path
 from os.path import join, splitext, exists, isfile, abspath
 
+from skbio.io import read
 from skbio.sequence import BiologicalSequence
 from biom.table import Table
 
-from qiime.util import get_qiime_library_version, load_qiime_config
+from qiime.util import get_qiime_library_version, load_qiime_config, qiime_open
 from qiime.colors import data_color_hsv
 
 """Contains formatters for the files we expect to encounter in 454 workflow.
@@ -601,7 +603,7 @@ def write_Fasta_from_name_seq_pairs(name_seqs, fh):
         raise ValueError("Need open file handle to write to.")
 
     for (name, seq) in name_seqs:
-        fh.write("%s\n" % BiologicalSequence(seq, id=name).to_fasta())
+        BiologicalSequence(seq, id=name).write(fh, format='fasta')
 
 
 def illumina_data_to_fastq(record_data, number_of_bases=None):
@@ -895,6 +897,68 @@ def format_fastq_record(label,
     return "@%s\n%s\n+\n%s\n" % (label, seq, qual)
 
 
+def write_synced_barcodes_fastq(joined_fp, index_fp, qual_score_variant='illumina1.8'):
+    """Writes new index file based on surviving assembled paired-ends.
+       -joined_fp : file path to paired-end assembled fastq file
+       -index_fp : file path to index / barcode reads fastq file
+       -qual_score_variant : format of fastq quality scores. Can be
+                            \'illumina1.3\' or \'illumina1.8\'
+
+       This function iterates through the joined reads file and index file.
+       Only those index-reads within the file at index_fp, that have headers
+       matching those within the joined-pairs at joined_fp, are written
+       to file.
+
+       Always forces output to be: illumina1.8
+
+     WARNING: Assumes reads are in the same order in both files,
+              except for cases in which the corresponding
+              read in the joined_fp file is missing (i.e. pairs
+              failed to assemble).
+
+    """
+
+    # open files (handles normal / gzipped data)
+    jh = qiime_open(joined_fp)
+    ih = qiime_open(index_fp)
+
+    # base new index file name on joined paired-end file name:
+    j_path, ext = path.splitext(joined_fp)
+    filtered_bc_outfile_path = j_path + '_barcodes.fastq'
+    fbc_fh = open(filtered_bc_outfile_path, 'w')
+
+    # Set up iterators
+    index_fastq_iter = read(ih, format='fastq', variant=qual_score_variant)
+    joined_fastq_iter = read(jh, format='fastq', variant=qual_score_variant)
+
+    # Write barcodes / index reads that we observed within
+    # the joined paired-ends. Warn if index and joined data
+    # are not in order.
+    for joined in joined_fastq_iter:
+        index = index_fastq_iter.next()
+        while joined.id != index.id:
+            try:
+                index = index_fastq_iter.next()
+            except StopIteration:
+                raise StopIteration("\n\nReached end of index-reads file" +
+                                    " before iterating through joined paired-end-reads file!" +
+                                    " Except for missing paired-end reads that did not survive" +
+                                    " assembly, your index and paired-end reads files must be in" +
+                                    " the same order! Also, check that the index-reads and" +
+                                    " paired-end reads have identical headers. The last joined" +
+                                    " paired-end ID processed was:\n\'%s\'\n" % (joined.id))
+        else:
+            # force output to illumina1.8
+            index.write(fbc_fh, format='fastq', variant='illumina1.8')
+
+    ih.close()
+    jh.close()
+    fbc_fh.close()
+
+    return filtered_bc_outfile_path
+
+
+
 HTML_LINES_INIT = """<html>
 <head>
 
diff --git a/qiime/join_paired_ends.py b/qiime/join_paired_ends.py
index a9d935c739..d4ae621b6a 100644
--- a/qiime/join_paired_ends.py
+++ b/qiime/join_paired_ends.py
@@ -8,11 +8,8 @@
 __maintainer__ = "Mike Robeson"
 __email__ = "robesonms@ornl.gov"
 
-from skbio.parse.sequences import parse_fastq
-from skbio.format.sequences import format_fastq_record
 from bfillings.fastq_join import FastqJoin, join_paired_end_reads_fastqjoin
 from bfillings.seqprep import SeqPrep, join_paired_end_reads_seqprep
-from qiime.util import qiime_open
 import os
 import gzip
 
@@ -21,57 +18,4 @@
                      'SeqPrep': join_paired_end_reads_seqprep}
 
 
-def write_synced_barcodes_fastq(joined_fp, index_fp):
-    """Writes new index file based on surviving assembled paired-ends.
-       -joined_fp : file path to paired-end assembled fastq file
-       -index_fp : file path to index / barcode reads fastq file
 
-       This function iterates through the joined reads file and index file.
-       Only those index-reads within the file at index_fp, that have headers
-       matching those within the joined-pairs at joined_fp, are written
-       to file.
-
-     WARNING: Assumes reads are in the same order in both files,
-              except for cases in which the corresponding
-              read in the joined_fp file is missing (i.e. pairs
-              failed to assemble).
-
-    """
-
-    # open files (handles normal / gzipped data)
-    jh = qiime_open(joined_fp)
-    ih = qiime_open(index_fp)
-
-    # base new index file name on joined paired-end file name:
-    j_path, ext = os.path.splitext(joined_fp)
-    filtered_bc_outfile_path = j_path + '_barcodes.fastq'
-    fbc_fh = open(filtered_bc_outfile_path, 'w')
-
-    # Set up iterators
-    index_fastq_iter = parse_fastq(ih, strict=False)
-    joined_fastq_iter = parse_fastq(jh, strict=False)
-    # Write barcodes / index reads that we observed within
-    # the joined paired-ends. Warn if index and joined data
-    # are not in order.
-    for joined_label, joined_seq, joined_qual in joined_fastq_iter:
-        index_label, index_seq, index_qual = index_fastq_iter.next()
-        while joined_label != index_label:
-            try:
-                index_label, index_seq, index_qual = index_fastq_iter.next()
-            except StopIteration:
-                raise StopIteration("\n\nReached end of index-reads file" +
-                                    " before iterating through joined paired-end-reads file!" +
-                                    " Except for missing paired-end reads that did not survive" +
-                                    " assembly, your index and paired-end reads files must be in" +
-                                    " the same order! Also, check that the index-reads and" +
-                                    " paired-end reads have identical headers. The last joined" +
-                                    " paired-end ID processed was:\n\'%s\'\n" % (joined_label))
-        else:
-            fastq_string = format_fastq_record(index_label, index_seq, index_qual)
-            fbc_fh.write(fastq_string)
-
-    ih.close()
-    jh.close()
-    fbc_fh.close()
-
-    return filtered_bc_outfile_path
diff --git a/scripts/join_paired_ends.py b/scripts/join_paired_ends.py
index e03e18fead..9041cb6a32 100755
--- a/scripts/join_paired_ends.py
+++ b/scripts/join_paired_ends.py
@@ -9,8 +9,8 @@
 __email__ = "robesonms@ornl.gov"
 
 from qiime.join_paired_ends import (join_method_names,
-                                    join_method_constructors,
-                                    write_synced_barcodes_fastq)
+                                    join_method_constructors)
+from qiime.format import write_synced_barcodes_fastq
 from qiime.util import (parse_command_line_parameters, get_options_lookup,
                         make_option, load_qiime_config, create_dir)
 import os
@@ -114,7 +114,14 @@
                 help='Only applies to SeqPrep method, otherwise ignored.' +
                       ' Set if input reads are in phred+64 format. Output will '
                       'always be phred+33. [default: %default]',
-                default=False)]
+                default=False),
+    make_option('-q', '--qual_score_variant',
+                help=' Input format of fastq data. Can be: \'illumina1.3\' or'+
+                    ' \'illumina1.8\'. Only used if using the \'-b\' option.' +
+                      ' Output will always be \'illumina1.8\'.' +
+                      '[default: %default]. For more info see: '+
+                      'http://scikit-bio.org/docs/latest/generated/skbio.io.fastq.html',
+                default='illumina1.8')]
 
 script_info['version'] = __version__
 
@@ -127,6 +134,7 @@ def main():
     forward_reads_fp = opts.forward_reads_fp
     reverse_reads_fp = opts.reverse_reads_fp
     pe_join_method = opts.pe_join_method
+    qual_score_variant=opts.qual_score_variant
     output_dir = opts.output_dir
     # fastq-join only options:
     perc_max_diff = opts.perc_max_diff
@@ -168,7 +176,7 @@ def main():
     if opts.index_reads_fp:
         index_reads = opts.index_reads_fp
         assembly_fp = paths['Assembled']  # grab joined-pairs output path
-        write_synced_barcodes_fastq(assembly_fp, index_reads)
+        write_synced_barcodes_fastq(assembly_fp, index_reads, qual_score_variant=qual_score_variant)
 
 
 if __name__ == "__main__":
diff --git a/tests/test_format.py b/tests/test_format.py
index 91a16d980c..fcc55a0f25 100755
--- a/tests/test_format.py
+++ b/tests/test_format.py
@@ -6,7 +6,7 @@
 __copyright__ = "Copyright 2011, The QIIME Project"  # consider project name
 __credits__ = [
     "Rob Knight", "Jeremy Widmann", "Jens Reeder", "Daniel McDonald",
-    "Jai Ram Rideout", "Jose Antonio Navas Molina"]
+    "Jai Ram Rideout", "Jose Antonio Navas Molina","Mike Robeson"]
 # remember to add yourself if you make changes
 __license__ = "GPL"
 __version__ = "1.8.0-dev"
@@ -20,7 +20,7 @@
 from numpy import array, nan, array_equal
 from skbio.util import remove_files
 from unittest import TestCase, main
-from skbio.parse.sequences import parse_fasta
+from skbio.io import read
 from qiime.util import  get_qiime_library_version
 from qiime.parse import fields_to_dict, parse_mapping_file
 from qiime.format import (format_distance_matrix, build_prefs_string,
@@ -33,7 +33,8 @@
                           format_p_value_for_num_iters, format_mapping_file, illumina_data_to_fastq,
                           format_mapping_html_data, format_te_prefs,
                           format_tep_file_lines, format_jnlp_file_lines,
-                          format_fastq_record, format_histograms_two_bins)
+                          format_fastq_record, format_histograms_two_bins,
+                          write_synced_barcodes_fastq)
 from biom.parse import parse_biom_table
 from biom.table import Table
 from StringIO import StringIO
@@ -81,6 +82,42 @@ def setUp(self):
                            (-0.1, 0.2)),
                           ('S3', 'T3', 100.68, 0.9, 1, 1, 1, (-0.4, -0.2))]
         self.corr_vec3 = [('S1', 'T1', 0.7777777777, 0, 0, 0, 0, (None, None))]
+        
+        # For testing `write_synced_barcodes_fastq`
+        # store files:
+        # joined_pairs
+        fd,self.joined_pe_fp = mkstemp(prefix='joined_', suffix='.fastq')
+        close(fd)
+        self.joined_pe = open(self.joined_pe_fp,'w')
+        self.joined_pe.write(joined_reads)
+        self.joined_pe.close()
+        self.files_to_remove.append(self.joined_pe_fp)
+
+        # all barcodes
+        fd,self.all_barcodes_fp = mkstemp(prefix='all_bc_', suffix='.fastq')
+        close(fd) 
+        self.all_barcodes = open(self.all_barcodes_fp,'w')       
+        self.all_barcodes.write(all_barcodes)
+        self.all_barcodes.close()
+        self.files_to_remove.append(self.all_barcodes_fp)
+
+        # out-of-order barcodes
+        fd,self.ooo_barcodes_fp = mkstemp(prefix='ooo_bc_',suffix='.fastq')
+        close(fd)
+        self.ooo_barcodes = open(self.ooo_barcodes_fp,'w')
+        self.ooo_barcodes.write(all_barcodes_out_of_order)
+        self.ooo_barcodes.close()
+        self.files_to_remove.append(self.ooo_barcodes_fp)
+
+        # missing barcodes
+        fd,self.missing_barcodes_fp = mkstemp(prefix='missing_bc_', suffix='.fastq')
+        close(fd)        
+        self.missing_barcodes = open(self.missing_barcodes_fp,'w')
+        self.missing_barcodes.write(missing_barcodes)
+        self.missing_barcodes.close()
+        self.files_to_remove.append(self.missing_barcodes_fp)
+
+
 
     def tearDown(self):
         remove_files(self.files_to_remove)
@@ -441,7 +478,7 @@ def test_write_Fasta_from_name_seqs_pairs(self):
         fh = open(tmp_filename, "w")
         write_Fasta_from_name_seq_pairs(seqs, fh)
         fh.close()
-        actual_seqs = list(parse_fasta(open(tmp_filename, "U")))
+        actual_seqs = [(rec.id, rec.sequence) for rec in (read(tmp_filename, format='fasta'))]
         remove(tmp_filename)
 
         self.assertEqual(actual_seqs, seqs)
@@ -696,6 +733,40 @@ def test_format_fastq_record(self):
         expected_lines = '@test_label\nAATTCCGG\n+\n12345678\n'
 
         self.assertEqual(actual_lines, expected_lines)
+    
+    # tests for writing barcodes of surviving joined paired ends.
+    def test_write_synced_barcodes_fastq(self):
+        """write_synced_barcodes_fastq: should work properly.
+           This function expects the barcodes.fastq and joined_pairs.fastq
+           files to be in the same order except for those missing data
+           that could not be joined. That is, not all paired-ends will
+           assemble.
+        """
+        filtered_bc_path = write_synced_barcodes_fastq(
+            self.joined_pe_fp,
+            self.all_barcodes_fp)
+
+        observed_barcodes = open(filtered_bc_path, 'U').read()
+        self.assertEqual(observed_barcodes, synced_barcodes)
+
+        remove(filtered_bc_path)
+
+    def test_out_of_order_barcodes(self):
+        """write_synced_barcodes_fastq: should fail if barcodes out of order
+           By out of order I mean that the data in the barcodes file
+           are not in the same order as the data within the joined paired-ends
+           file.
+        """
+        self.assertRaises(StopIteration, write_synced_barcodes_fastq,
+                          self.joined_pe_fp,
+                          self.ooo_barcodes_fp)
+
+    def test_missing_barcodes(self):
+        """"write_synced_barcodes_fastq: should fail if barcodes are missing."""
+        self.assertRaises(StopIteration, write_synced_barcodes_fastq,
+                          self.joined_pe_fp,
+                          self.missing_barcodes_fp)
+    
 
 
 example_mapping_file = """#SampleID\tcol1\tcol0\tDescription
@@ -897,6 +968,391 @@ def test_format_fastq_record(self):
 </jnlp>
 """
 
+all_barcodes = """@MISEQ03:64:000000000-A2H3D:1:1101:14358:1530 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:14206:1564 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:14943:1619 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:15764:1660 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:15211:1752 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:15201:1774 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:15976:1791 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:16031:1840 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:12964:1852 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:17245:1906 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:18171:1983 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:14225:2009 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:16656:2052 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:18209:2060 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:13824:2095 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:17839:2106 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:17831:2124 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:12555:2129 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:13627:2170 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:11781:2223 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:17996:2254 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:13712:2276 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:15819:2301 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:11958:2304 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:19110:2311 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+"""
+
+all_barcodes_out_of_order = """@MISEQ03:64:000000000-A2H3D:1:1101:14358:1530 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:14206:1564 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:14943:1619 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:15764:1660 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:15976:1791 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:16031:1840 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:12964:1852 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:17245:1906 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:18171:1983 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:14225:2009 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:16656:2052 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:18209:2060 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:15211:1752 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:15201:1774 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:13824:2095 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:17839:2106 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:17831:2124 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:12555:2129 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:13627:2170 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:11781:2223 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:17996:2254 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:13712:2276 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:15819:2301 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:11958:2304 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:19110:2311 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+"""
+
+missing_barcodes = """@MISEQ03:64:000000000-A2H3D:1:1101:14358:1530 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:14206:1564 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:14943:1619 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:15764:1660 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:15211:1752 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:15201:1774 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:15976:1791 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:16031:1840 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:12964:1852 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:17245:1906 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:18209:2060 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:13824:2095 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:17839:2106 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:17831:2124 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:12555:2129 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:13627:2170 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:11781:2223 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:17996:2254 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:13712:2276 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:15819:2301 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:11958:2304 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:19110:2311 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+"""
+joined_reads = """@MISEQ03:64:000000000-A2H3D:1:1101:14358:1530 1:N:0:TCCACAGGAGT
+TNCAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGTTAAGTTGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACAAGCTAGAGTATGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGTGAAATGCGTAGATATAGGAAGGAACACCAGTGGCGAAGGCGACCACCTGGACTGATACTGACACTGAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGAAACCCTTGTAGTCCGT
++
+?#5<????DDDDDDDDEEEEFFHHHHHHHHHHHHHHDCCHHFGDEHEH>CCE5AEEHHHHHHHHHHHHHHHHHFFFFHHHHHHEEADEEEEEEEEEEEEEEEEEEEEEEE?BEEEEEEEEEEEAEEEE0?A:?EFCAC==ECEEFFEFEEFBACEEDD=8CDDDEDFFFDFFHHHFHHFAFDHFCHHFHHHHHHEDCHHIHFECIIIIIHHHHGGDIHHGIHIIHFHHHHHIIIHHHEHHHHGFIIIIIIIIHFFCFFCBBDDDBDDB@@?????
+@MISEQ03:64:000000000-A2H3D:1:1101:14206:1564 1:N:0:TCCACAGGAGT
+TACGTAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTTTTGTAAGTCAGATGTGAAAGCCCCGGGCTCAACCTGGGAACTGCGTTTGAAACTACAAGGCTAGAGTGTAGCAGAGGGGGGTAGAATTCCACGTGTAGCAGTGAAATGCGTAGAGATGTGGAGGAATACCAATGGCGAAGGCAGCCCCCTGGGTTAACACTGACGCTCATGCACGAAAGCGTGGGGAGCAAACAGGATTAGAAACCCCTGTAGTCCGT
++
+?????BB?DDDDDD@DDCEEFFH>EEFHHHHHHGHHHCEEFFDC5EECCCCCCDECEHF;?DFDDFHDDBBDF?CFDCCFEAA@?:;EEEEEEEECBA,BBE?EEAAECA0:?C?:??A:8*:00?0**:8:DDECDD0.?:????:,:?EEEEEE??44BEEEEEDDBD=EEB==FFFDFDFD?FFEE:EEFFFDFFECCDHHHHEHHHHHHHFBHHHDCGBHF@HFFDEHFF@HHHHHHHHHHHFFHHHHHFFFFFC@?DDDBDDB@@?????
+@MISEQ03:64:000000000-A2H3D:1:1101:14943:1619 1:N:0:TCCACAGGAGT
+TACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGTTAAGTTGGATGTGAAAGCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACAAGCTAGAGTATGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGTGAAATGCGTAGATATAGGAAGGAACACCAGTGGCGAAGGCGACCACCTGGACTGATACTGACACTGAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCCTGTAGTCCGT
++
+?AAAABBADDDEDEDDGGGGGGIIHHHIIIIIIIHHHCCHHFFEFHHHDCDH5CFHIIHIIIIHHHHHHHHHHHHHHHHHHHGGGEGGGGDDEGEGGGGGGGGGGGGGGEEEGCCGGGGGGEGCEEEECEAECGFEEFEACEEGGGEEEFECE<BEDFFFEEEEFFFFFFFFHFHFHFHFHEFFCEFHHDHHIIHHHHHGEFE?IIIIIIHIHHIIHHHIHHHHHHHHHHHHHHHHHHIHIIIIHIIHIHHIIFFFFFFA?DDDDDDB@@?????
+@MISEQ03:64:000000000-A2H3D:1:1101:15764:1660 1:N:0:TCCACAGGAGT
+TACGAAGGGGGCTAGCGTTGCTCGGAATCACTGGGCGTAAAGCGCACGTAGGCGGATTGTTAAGTCAGGGGTGAAATCCTGGAGCTCAACTCCAGAACTGCCTTTGATACTGGCGATCTTGAGTCCGGGAGAGGTGAGTGGAACTGCGAGTGTAGAGGTGAAATTCGTAGATATTCGCAAGAACACCAGTGGCGAAGGCGGCTCACTGGCCCGGTACTGACGCTGAGGTGCGAAAGCTAGGGGAGCAAACAGGATTAGATACCCCGGTAGTCCGT
++
+???????@DDDDDDBDFEEFEFHEHHHHHHHHHHHHHEHHHHFEHHHHAEFHGEHAHHHHHHHHHHHHHHH=@FEFEEFEFEDAEEEFFE=CEBCFFFCECEFEFFFCEEEFFCD>>FFFEFF*?EED;?8AEE08*A?A:?EA;?EEEEE??:CBBE?EEEFEEE?BCE?;CE?=EDEE=EECEFE?C0DD8D4C<DEFD?@5,FHHHCHHFEBC@HHDHHGFFCCHHEDCA?E=HFDHHGC=HHFCHCFCECFFCA>?<BBBB?BB=@?????
+@MISEQ03:64:000000000-A2H3D:1:1101:15201:1774 1:N:0:TCCACAGGAGT
+TACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGTTAAGTTGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACAAGCTAGAGTATGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGTGAAATGCGTAGATATAGGAAGGAACACCAGTGGCGAAGGCGACCACCTGGACTGATACTGACACTGAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGAAACCCCGGTAGTCCGT
++
+?????BB?DDDDDDBDEEEEFFHFHHHHHHHHHHHFH>CEHDGDDCDE5CCEACFHHHHHHHHFFHHHHHHHHFHHFHHHHHHDEBFEEE@DEEEEEEEEEEEEEEBBCBECEEEEEEEEEEEEEEECACCEEEEEEA00E?EEEBAEEEE?>?CEDDC?B?A:EDEEDEDEFFBFFFDFD@DEEEFHHDDD+HDDECDDEDGFBHHFHFFHHHGCFGEEEEGHHFHHHHHHHHHHHEFEHHGDHHECFCFHFFFFFFC=<BBBBBBB=@?????
+@MISEQ03:64:000000000-A2H3D:1:1101:14225:2009 1:N:0:TCCACAGGAGT
+TACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGTTAAGTTGGATGTGAAAGCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACAAGCTAGAGTATGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGTGAAATGCGTAGATATAGGAAGGAACACCAGTGGCGAAGGCGACCACCTGGACTGATACTGACACTGAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCCTGTAGTCCGT
++
+?????BB?DDDDDDBDEEEEFFHHHHIIIIHHIIIIHHEHIFGEHHHHCCEHAEFHIIHIIIIHHHHHHHHHHFHHHHHHHHFFFEFFFFFEFFFFFFEFFFFFFEFFFEFCACFFFFFFFAEFEFEEA?:AAEE<BFEEECCEFFEEEEFEEEFEEDD=DEEDEEFFFFFFFHHHHHHFFDFFFHHHHDHHHHEDEHHGEFFFIIIHIHIIHHHHHIHHHIHHFFHHHHHHIHHHHHIHIIHIIIIHHHHIHFFFFFC??DDDDDDB@@?????
+@MISEQ03:64:000000000-A2H3D:1:1101:16656:2052 1:N:0:TCCACAGGAGT
+TACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGTTAAGTTGGATGTGAAAGCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACAAGCTAGAGTATGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGTGAAATGCGTAGATATAGGAAGGAACACCAGTGGCGAAGGCGACCACCTGGACTGATACTGACACTGAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCGGGTAGTCCGT
++
+?????BB?BDDDDDDDGFFEGGIIHHIIIIIHHHHIHCCFFDEEEHEHFFEH5AFHHIHIHIHGGHHHHHHHFHHFHHHHHHGEGFEGEGGEGGGGCEGGEGGGGEGGEFECGGGGGGGGEGGECEGG?CCCEGC08?50=?EGGBEFFFFEB@EAEEFDDDEDBCFFBF?DFFFFHFHFF;HFFHHHHHED;HDEDD<HEFHGHIIIHHIIHFFHHHFAHHFIIHHHHECHFHHHHHIHHHHHHHFHHFHHIFFFFFC@<DDDDDDB@@?????
+@MISEQ03:64:000000000-A2H3D:1:1101:12555:2129 1:N:0:TCCACAGGAGT
+TACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTCGTTAAGTTGGATGTGAAAGCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACGAGCTAGAGTATGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGTGAAATGCGTAGATATAGGAAGGAACACCAGTGGCGAAGGCGACCACCTGGACTGATACTGACACTGAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGAAACCCCGGTAGTCCGT
++
+????ABBADDDDDEDDGGGGGGIIHHIIIIIHIIHHHFFHHHFHHHHH>CDHAEFHFGHHFHHHHHHHHHFHHFHFFHHHHHGBEEAD;DGGGGEGGGCGCEEEGEGGGCEA>>CEDGDGE:C:CGGG:AC??EEA8C::AECEGEGCCECEEGGGGGEBCECE@CEFEDFEFFFFFFFBF@HHHHHHHHHHHHDEHEHHHHFDHIIIHIFHF=IHFHIHIHHGFIHHHHEHFHEHHHHHIIHHHIIIHFHHHFFFFFEDDDDDDDDB@@?????
+@MISEQ03:64:000000000-A2H3D:1:1101:11781:2223 1:N:0:TCCACAGGAGT
+TACGTAGGGCGCAAGCGTTATCCGGAATTATTGGGCGTAAAGAGCTCGTAGGCGGTTTGTCGCGTCTGCCGTGAAAGTCCGGGGCTCAACTCCGGATCTGCGGTGGGTACGGGCAGACTAGAGTGATGTAGGGGAGATTGGAATTCCTGGTGTAGCGGTGAAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGGTCTCTGGGCATTAACTGACGCTGAGGAGCGAAAGCATGGGGAGCGAACAGGATTAGATACCCCAGTAGTCCGT
++
+???A?BB?DDDDDDDDEEECFFHHHHHIHHHIIIHHHECEHFCFHGGH>CFEFEHHHHHFFDFHCDEFFHHEBFFFF?BBEEEEEEEFFFBEEEEAEDEFEDD.?EA4ACEDDDECEFFFFEF:*::?ACCFFD8<AE?EFFFF:EEEEFFFA<EEDD,.DD?CEFFFDDDFFHDBHFFFDEEFFFE@8EEEFGACEFEHFFE;DDHHHHGFHHHHHEHHHHFHHHEEDEHHHHHHFDHEHEHHHHHHHHHHHFFFFFCDBDDDDDDB@@?????
+@MISEQ03:64:000000000-A2H3D:1:1101:15819:2301 1:N:0:TCCACAGGAGT
+TACGTAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTGAGTTAAGTCTGCTGTGAAAGCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACAAGCTAGAGTATGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGTGAAATGCGTAGATATAGGAAGGAACACCAGTGGCGAAGGCGACCACCTGGACTGATACTGACACTGAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGAAACCCCGGTAGTCCGT
++
+?????BB?DEDDDDDDFDEEFFHHHEFHHIIIIIIHHCHHFHHHCEEACCHHHEH)<<CCDGFFDFFFBCB@DFHFHFHHEEFB8@EEEFFEEFFFFFFFFFEFCEFFFCAAC?EF??AC???AA:?E::::?EE80EEC:?EEFEEFECFEEBEEEDC=CEEDEEDEEFDEFFDFFBFDFDHFCDHHD+HHHHD@HHFHHHF?FDBHHHHHHHHFHHGCF?DGDEHHHHEGFHEHHHHHHHGFHHHFFBHHHFFFFFC@<DDDDDDB=@???9?
+@MISEQ03:64:000000000-A2H3D:1:1101:19110:2311 1:N:0:TCCACAGGAGT
+TACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGTTAAGTTGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACAAGCTAGAGTATGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGTGAAATGCGTAGATATAGGAAGGAACACCAGTGGCGAAGGCGACCCCCTGGACTGATACTGACACTGAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCGT
++
+????9BB?BBBBBBBBEEECFAFHHHHHHHFHHHHHHCCEFF/CDCCE>DCH5AECFHHHFHHHHHHHHHHHGFHHCFHHHHHEEEDEDEED@EEEEEEEEEEEEEEEEE?;BEEE?EEEEEE?*?CA?EE:EA?'8C*:1?CEEECAAECA:CEEFFECEEEEEEEBEFFEEEEA??DDB?FFEHHFHEEHFFHDDCCC5*5+DHHFA5FA5-HHHHHGFAGHHHHHHHEHFHEEHHHHHHHFGC>FHHHHHFFFFFC5<DDDDDDB=@?????
+"""
+
+synced_barcodes = """@MISEQ03:64:000000000-A2H3D:1:1101:14358:1530 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:14206:1564 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:14943:1619 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:15764:1660 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:15201:1774 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:14225:2009 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:16656:2052 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:12555:2129 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:11781:2223 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:15819:2301 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+@MISEQ03:64:000000000-A2H3D:1:1101:19110:2311 1:N:0:TCCACAGGAGT
+TCCACAGGAGT
++
+FFFFFFFFFFF
+"""
+
 
 # run unit tests if run from command-line
 if __name__ == '__main__':
diff --git a/tests/test_join_paired_ends.py b/tests/test_join_paired_ends.py
deleted file mode 100644
index 8ddde33420..0000000000
--- a/tests/test_join_paired_ends.py
+++ /dev/null
@@ -1,701 +0,0 @@
-#!/usr/bin/env python
-# file: test_join_paired_ends.py
-"""Tests of code for joining paired-end reads"""
-
-__author__ = "Mike Robeson"
-__copyright__ = "Copyright 2013, The QIIME Project"
-__credits__ = ["Mike Robeson"]
-__license__ = "GPL"
-__version__ = "1.8.0-dev"
-__maintainer__ = "Mike Robeson"
-__email__ = "robesonms@ornl.gov"
-
-
-import os
-import shutil
-from tempfile import mkdtemp, NamedTemporaryFile
-
-from unittest import TestCase, main
-from qiime.join_paired_ends import write_synced_barcodes_fastq
-
-
-class JoinPairedEndsTests(TestCase):
-
-    """Tests for join_paired_ends."""
-
-    def setUp(self):
-        """set up files to be used in all tests"""
-
-        # set up temp directory that all temp files will
-        # be written to:
-        self.temp_dir_path = mkdtemp()
-
-        # store files:
-        # joined_pairs
-        self.joined_pe = NamedTemporaryFile(prefix='joined_',
-                                            suffix='.fastq',
-                                            dir=self.temp_dir_path,
-                                            delete=False)
-        self.jpe_fp = self.joined_pe.name
-        self.joined_pe.write(joined_reads)
-        self.joined_pe.close()
-
-        # all barcodes
-        self.all_barcodes = NamedTemporaryFile(prefix='all_bc_',
-                                               suffix='.fastq',
-                                               dir=self.temp_dir_path,
-                                               delete=False)
-        self.all_bc_fp = self.all_barcodes.name
-        self.all_barcodes.write(all_barcodes)
-        self.all_barcodes.close()
-
-        # out of order barcodes
-        self.ooo_barcodes = NamedTemporaryFile(prefix='ooo_bc_',
-                                               suffix='.fastq',
-                                               dir=self.temp_dir_path,
-                                               delete=False)
-        self.ooo_bc_fp = self.ooo_barcodes.name
-        self.ooo_barcodes.write(all_barcodes_out_of_order)
-        self.ooo_barcodes.close()
-
-        # missing barcodes
-        self.missing_barcodes = NamedTemporaryFile(prefix='missing_bc_',
-                                                   suffix='.fastq',
-                                                   dir=self.temp_dir_path,
-                                                   delete=False)
-        self.missing_bc_fp = self.missing_barcodes.name
-        self.missing_barcodes.write(missing_barcodes)
-        self.missing_barcodes.close()
-
-    def tearDown(self):
-        """Remove all temp files"""
-        shutil.rmtree(self.temp_dir_path)
-
-    def test_write_synced_barcodes_fastq(self):
-        """write_synced_barcodes_fastq: should work properly.
-           This function expects the barcodes.fastq and joined_pairs.fastq
-           files to be in the same order except for those missing data
-           that could not be joined. That is, not all paired-ends will
-           assemble.
-        """
-        filtered_bc_path = write_synced_barcodes_fastq(
-            self.jpe_fp,
-            self.all_bc_fp)
-
-        observed_barcodes = open(filtered_bc_path, 'U').read()
-        self.assertEqual(observed_barcodes, synced_barcodes)
-
-        os.remove(filtered_bc_path)
-
-    def test_out_of_order_barcodes(self):
-        """write_synced_barcodes_fastq: should fail if barcodes out of order
-           By out of order I mean that the data in the barcodes file
-           are not in the same order as the data within the joined paired-ends
-           file.
-        """
-        self.assertRaises(StopIteration, write_synced_barcodes_fastq,
-                          self.jpe_fp,
-                          self.ooo_bc_fp)
-
-    def test_missing_barcodes(self):
-        """"write_synced_barcodes_fastq: should fail if barcodes are missing."""
-        self.assertRaises(StopIteration, write_synced_barcodes_fastq,
-                          self.jpe_fp,
-                          self.missing_bc_fp)
-
-
-all_barcodes = """@MISEQ03:64:000000000-A2H3D:1:1101:14358:1530 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:14206:1564 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:14943:1619 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:15764:1660 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:15211:1752 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:15201:1774 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:15976:1791 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:16031:1840 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:12964:1852 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:17245:1906 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:18171:1983 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:14225:2009 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:16656:2052 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:18209:2060 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:13824:2095 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:17839:2106 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:17831:2124 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:12555:2129 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:13627:2170 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:11781:2223 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:17996:2254 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:13712:2276 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:15819:2301 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:11958:2304 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:19110:2311 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-"""
-
-all_barcodes_out_of_order = """@MISEQ03:64:000000000-A2H3D:1:1101:14358:1530 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:14206:1564 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:14943:1619 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:15764:1660 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:15976:1791 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:16031:1840 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:12964:1852 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:17245:1906 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:18171:1983 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:14225:2009 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:16656:2052 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:18209:2060 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:15211:1752 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:15201:1774 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:13824:2095 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:17839:2106 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:17831:2124 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:12555:2129 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:13627:2170 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:11781:2223 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:17996:2254 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:13712:2276 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:15819:2301 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:11958:2304 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:19110:2311 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-"""
-
-missing_barcodes = """@MISEQ03:64:000000000-A2H3D:1:1101:14358:1530 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:14206:1564 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:14943:1619 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:15764:1660 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:15211:1752 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:15201:1774 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:15976:1791 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:16031:1840 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:12964:1852 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:17245:1906 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:18209:2060 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:13824:2095 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:17839:2106 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:17831:2124 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:12555:2129 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:13627:2170 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:11781:2223 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:17996:2254 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:13712:2276 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:15819:2301 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:11958:2304 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:19110:2311 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-"""
-
-
-# For reference. Data used to make the 'joined_reads' reference string.
-forward_reads = """@MISEQ03:64:000000000-A2H3D:1:1101:14358:1530 1:N:0:TCCACAGGAGT
-TNCAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGTTAAGTTGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACAAGCTAGAGTATGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGTGAAATGCGTAGATATAGGAAGGAACACCAGTGGCGAAGGCGACCACCTGGACTGAAACTGACACTGAGGGGCGAAAGCGGGGGGGGCAAACG
-+
-?#5<????DDDDDDDDEEEEFFHHHHHHHHHHHHHHDCCHHFGDEHEH>CCE5AEEHHHHHHHHHHHHHHHHHFFFFHHHHHHEEADEEEEEEEEEEEEEEEEEEEEEEE?BEEEEEEEEEEEAEEEE0?A:?EE)8;)0ACEEECECCECAACEE?>)8CCC?CCA8?88ACC*A*::A??:0?C?.?0:?8884>'.''..'0?8C?C**0:0::?ECEE?############################
-@MISEQ03:64:000000000-A2H3D:1:1101:14206:1564 1:N:0:TCCACAGGAGT
-TACGTAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTTTTGTAAGTCAGATGTGAAAGCCCCGGGCTCAACCTGGGAACTGCGTTTGAAACTACAAGGCTAGAGTGTAGCAGAGGGGGGTAGAATTCCACGTGTAGCGGTGAAATGCGTAGAGATGGGGAGGAATACCAATGGCGAAGGCAGCCCCCGGGGTTAACACTGACGCCAAGGCACGAAAGCGGGGGGGGCAAACG
-+
-?????BB?DDDDDD@DDCEEFFH>EEFHHHHHHGHHHCEEFFDC5EECCCCCCDECEHF;?DFDDFHDDBBDF?CFDCCFEA@@::;EEEEEEEECBA,BBE?:>AA?CA*:**0:??A:8*:*0*0**0*:?CE?DD'..0????:*:?*0?EC*'.)4.?A***00)'.00*0*08)8??8*0:CEE*0:082.4;**?AEAA?#############################################
-@MISEQ03:64:000000000-A2H3D:1:1101:14943:1619 1:N:0:TCCACAGGAGT
-TACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGTTAAGTTGGATGTGAAAGCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACAAGCTAGAGTATGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGTGAAATGCGTAGATATAGGAAGGAACACCAGGGGCGAAGGCGACCACCTGGACTGAAACTGACACTGAGGGGCGAAAGCGGGGGGGGCAAAAG
-+
-?AAAABBADDDEDEDDGGGGGGIIHHHIIIIIIIHHHCCHHFFEFHHHDCDH5CFHIIHIIIIHHHHHHHHHHHHHHHHHHHGGGEGGGGDDEGEGGGGGGGGGGGGGGEEEGCCGGGGGGEGCEEEECE?ECGE.84.8CEEGGGE:CCCC0:?C<8.48CC:C??.8.8?C:*:0:*9)??CCEE**)0'''42<2C8'8..8801**0*.1*1?:?EEEC?###########################
-@MISEQ03:64:000000000-A2H3D:1:1101:15764:1660 1:N:0:TCCACAGGAGT
-TACGAAGGGGGCTAGCGTTGCTCGGAATCACTGGGCGTAAAGCGCACGTAGGCGGATTGTTAAGTCAGGGGTGAAATCCTGGAGCTCAACTCCAGAACTGCCTTTGATACTGGCGATCTTGAGTCCGGGAGAGGTGAGTGGAACTGCGAGTGTAGAGGTGAAATTCGTAGATATTCGCAAGAACACCAGTGGCGAAGGCGGCTCACTGGCCCGGAACTGACGCTGAGGGGCGAAAGCTGGGGGAGCAAACG
-+
-???????@DDDDDDBDFEEFEFHEHHHHHHHHHHHHHEHHHHFEHHHHAEFHGEHAHHHHHHHHHHHHHHH=@FEFEEFEFEDAEEEFFE=CEBCFFFCECEFEFFFCEEEFFCD>>FFFEFF*?EED;?8AEE08*A*1)?E::???;>2?*01::A?EEEFEEE?:C.8:CE?:?8EE8AECEFE?C0::8'488DE>882)*1?A*8A########################################
-@MISEQ03:64:000000000-A2H3D:1:1101:15211:1752 1:N:0:TCCACAGGAGT
-TACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGTTAAGTTGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACAAGCTAGAGTATGGTAGAGGGGGGTGGAATTTCCTGTGTAGCGGGGAAATGCGTAGATATGGGAAGGAACACCAGGGGCGAAGGCGACCACCTGGACTGATACTGACACTGGGGTGGGAAAGGGGGGGGAGGAAAAG
-+
-?????<B?DBBDDDBACCEEFFHFHHHHHHHHHHHHH5>EFFFEAACEC7>E5AFEFHHHHHHF=GHFGHFHHHHFHFHH;CED8@DDDE=4@EEEEECE=CECECEECCBB34,=CAB,40:?EEEE:?AAAE8'.4'..8*:AEEECCCA::A################################################################################################
-@MISEQ03:64:000000000-A2H3D:1:1101:15201:1774 1:N:0:TCCACAGGAGT
-TACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGTTAAGTTGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACAAGCTAGAGTATGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGGGAAATGCGTAGATATAGGAAGGAACACCAGTGGCGAAGGCGACCACCTGGACTGATACTGACACTGAGGTGCGAAAGCGGGGGGGGCAAACG
-+
-?????BB?DDDDDDBDEEEEFFHFHHHHHHHHHHHFH>CEHDGDDCDE5CCEACFHHHHHHHHFFHHHHHHHHFHHFHHHHHHDEBFEEE@DEEEEEEEEEEEEEEBBCBECEEEEEEEEEEEEEEE?ACCEEEA)84)0.?EEE:AEACA?0?CEDD'.4?A:ACA)0'80:A:?*0*0)8CEEEEE?*0*)88888A'.5;2A)*0000*8:*0:?CEEEE?A*?A#######################
-@MISEQ03:64:000000000-A2H3D:1:1101:15976:1791 1:N:0:TCCACAGGAGT
-TACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTCGTTAAGTTGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACAAGCTAGAGTATGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGGGAAATGCGTAGATATGGGAAGGAACACCGGGGGGGAGGGGGGCTCTCGGGTCCTTTTCGGCGGCTGGGGGCGGAAGGCAGGGGGGGCAACCG
-+
-?????BB?DDDDDDDDEEEEFFIFHHHHHHIIIHIFHCCHF@F>CECHCDDECCFEADEHHHHHHHHFGHHHHHHFHHHHHHF8:<DEEEADEEFFFFFFABEFFEFFECBCEEFEFFFFEACEEEEE*10*1??.08.888AEF?EEEC1:1:??>>'88AC?::?AA##################################################################################
-@MISEQ03:64:000000000-A2H3D:1:1101:16031:1840 1:N:0:TCCACAGGAGT
-TACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGTTAAGTTGGATGTGAAAGCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACAAGCTAGAGTATGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGGGAAATGCGTAGATATAGGAAGGAACACCAGGGGCGAAGGCGACCACCTGGACGGATACTGACACTGAGGGGCGAAAGGGTGGGGAGAAAAAG
-+
-?????BB?DDDDDDDDGFEGGGIHHHHIIIIIIIHFE>CFFFFDCHCH>>CE-5EEIIHHHIHHHHHHHHHHGHFDFHFHEHGBEEEEGGEDGGGGEGGEGGGGGCEGCCEEGGG><CEECCGCEEEG?C:1?EG.8<.88CCCEEGE?C?C*:1:<>'.8?8:C:?00.0?:?*1::*9CC?EEEG*?##############################################################
-@MISEQ03:64:000000000-A2H3D:1:1101:12964:1852 1:N:0:TCCACAGGAGT
-TNCAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGCAAAGCGCGCGTAGGTGGTTTGTTAAGTTGGATGTGAAAGCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACAAGCTAGAGTATGGTAGAGGGTGGTGGAATTTCCTGTGAAGCGGGGAAATGCGTAGATATAGGAAGGAACACCAGGGGCGAAGGCAACCACCGGGACTGAAACTGAACCGGAGGGGGGAAAGCGGGGGGGGAAAACG
-+
-?#55????DDDDDDDDEEEEFFHHBHHHFFGHHFHDC+5>C/?E7DCHCCCD5AECFHHHFHHHHHHHHHFFFFFHFFDFEFF5)@=DEFDEFEEFF;AEAABC,4BECCC=B,5?C8?CC?CC*:?E010:?EA)0.)08C?A:?A########################################################################################################
-@MISEQ03:64:000000000-A2H3D:1:1101:17245:1906 1:N:0:TCCACAGGAGT
-TACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGTTAAGTTGGATGTGAAAGCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACAAGCTAGAGTATGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGTGAAATGCGTAGATATAGGAGGGAACACAAGGGGCGAAGGCGACCACCGGGACGGAAACTGCAACTGGGGGGGGAAAGCGGGGGGGGAAACAG
-+
-AAA??BB?DDDDDDDDGGEGGGIHGHIIIIIIHF?CFCCDFFFDCHEHC>DH5AFEHIHHHHHHHHHHHHHHFFFFFHHHHHGDBEEGGGGGGG@EGEGGGGGGGCGEGACC>EGEGGGGC:C0CEEG:0::CEE)88)08?:CECCE:C*10*104A.4CE:*:?C8)'8CC##############################################################################
-@MISEQ03:64:000000000-A2H3D:1:1101:18171:1983 1:N:0:TCCACAGGAGT
-GACGTAGGAGGCGAGCGTTGTCCGGATTCATTGGGCGTAAAGAGCGCGCAGGCGGCTTGGTAAGTCGGATGTGAAATCCCGAGGCTCAACCTCGGGTCTGCATCCGATACTGCCCGGCTAGAGGTAGGTAGGGGAGATCGGAATTCCTGGTGTAGCGGTGAAATGCGCAGATATCAGGAGGAACACCGGGGGCGAAGGCGGATCTCTGGGCCTTCCCTGACGCTCAGGCGCGAAAGCGGGGGGGGCGAACG
-+
-??????B?DDDDDDDDFFEFFFIHFEEEHHIHHHFHHEHHFGFFFHCEHEHCDECCEFFE4DDFDBEEEEEFFFFEEFFCE8B>BEFEEFFCEFE>8>EFFE*A?A?ADDAAEE8E>;>EA:??1*:?111?C<88AA08?ACECF:*:?*08:0:8<.4?EE*A:))'..0*01*?:08?A*?CA#################################################################
-@MISEQ03:64:000000000-A2H3D:1:1101:14225:2009 1:N:0:TCCACAGGAGT
-TACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGTTAAGTTGGATGTGAAAGCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACAAGCTAGAGTATGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGTGAAATGCGTAGATATAGGAAGGAACACCAGTGGCGAAGGCGACCACCTGGACTGAAACGGACACTGAGGGGCGAAAGCGGGGGGGGCAAACG
-+
-?????BB?DDDDDDBDEEEEFFHHHHIIIIHHIIIIHHEHIFGEHHHHCCEHAEFHIIHIIIIHHHHHHHHHHFHHHHHHHHFFFEFFFFFEFFFFFFEFFFFFFEFFFEFCACEFFFFFF:C?CEEE*?:AAEE88;088?AEFCEAEECEEEFE>?).?ECCEEE8?4AFFE0?*0088ACFFFAAC*0?C888>>CD?D;8CE*:*:A?CF*::)0?DD?:::?########################
-@MISEQ03:64:000000000-A2H3D:1:1101:16656:2052 1:N:0:TCCACAGGAGT
-TACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGTTAAGTTGGATGTGAAAGCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACAAGCTAGAGTATGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGTGAAATGCGTAGATATAGGAAGGAACACCAGGGGCGAAGGCGACCACCGGGACTGAAACTGACACTGAGGGGGGAAAGCGGGGGGGGAAAACA
-+
-?????BB?BDDDDDDDGFFEGGIIHHIIIIIHHHHIHCCFFDEEEHEHFFEH5AFHHIHIHIHGGHHHHHHHFHHFHHHHHHGEG@EGEGGEGGGGCEGGEGGGGEGGACECGGGGGGGGEGGCCEGG?CCCEGC088)0.?EGG?EC*::C*:??<8.48?C:?C808.8CEE#############################################################################
-@MISEQ03:64:000000000-A2H3D:1:1101:18209:2060 1:N:0:TCCACAGGAGT
-TACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGTAGGCGGCTCAGCAAGTCAGGGGTGAAATCCCGGGGCTCAACCCCGGAACTGCCCTTGAAACTGCTAAGCTAGAATCTTGGAGAGGCGAGTGGAATTCCGAGTGTAGAGGGGAAATTCGTAGATATTCGGAAGAACACCAGGGGCGAAGGCGACCCCCTGGACAAGCATTGACGCTGAGGGGGGAAAGCGGGGGGGGCAAAAG
-+
-?????BB?BDDDDDDDECEEFFHHHHAHFHHHHHHHHCCHHH=@DEEHFHFCGHHB)?ECGHHH?DHHHHHCCCFFHHHFEEEEEEEEEEEEEB)>EDACEECEECEEECEE:*0A:AEAECA:0::ACE??E?.8'4.88?EC*00:08).0:*00?)..8AAAAA*0)0::?::?0A8)?C:?A#################################################################
-@MISEQ03:64:000000000-A2H3D:1:1101:13824:2095 1:N:0:TCCACAGGAGT
-TACGTAGGGGGCTAGCGTTGTCCGGAATCATTGGGCGTAAAGCGCGTGTAGGCGGCCCGGTAAGTCCGCTGTGAAAGTCGGGGGCTCAACCCTCGAAAGCCGGGGGATACTGTCGGGCTAGAGTACGGAAGAGGCGAGTGGAATTCCTGGTGTAGCGGTGAAATGCGCAGATATCAGGAGGAACACCCATTGCGAAGGCAGCTCGCTGGGACGTTACTGAGGCTGAGACCGGAAAGGGGGGGGGGCAAAAG
-+
-??A??BBADDDDDDBDFEEFFFHHHHHFHHHIHHFHHCCHHFHDCCDEEHHFIHAHHHHH@EFFDFFEBDEDEFFECBBEEEED?28CCFFECE;EF8?ECD;'488?EEFCE:A>>?>EECEE::A8E8.8?8).'.'08AEE*?:*::*001:?<D.'8??*:*))'''01***10*088CEEEEA8C#############################################################
-@MISEQ03:64:000000000-A2H3D:1:1101:17839:2106 1:N:0:TCCACAGGAGT
-TACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGTTAAGTTGGATGTGAAAGCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACAAGCTAGAGTATGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGTGAAATGCGTAGATATAGGAAGGAACACCAGTGGCGAAGGCGACAACCGGGACGGAAACTGACACTGAGGGGCGAAAGCGGGGGGGGCAAAAG
-+
-AAA?ABB?DDDDDDDEGFEGGFHIHHIIIIIIIIDFH5CFHHGHEH=DC>CE5AEEHFHIHIFHHHHHHHHHFHHFHHHHHHGGGGGEEGGGGGDEGGGGGGGGGGGGGCE>AEGEGGGGEEECEGEE1:??CEC08>.88CEEECG*:C?CC:?0.4.4CE?CECC?)4?CC:*11?:?)CCEGG).9*1:?8<2<<C####################################################
-@MISEQ03:64:000000000-A2H3D:1:1101:17831:2124 1:N:0:TCCACAGGAGT
-TACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGTTAAGTTGGATGTGAAAGCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACAAGCTAGAGTATGGTAGAGGGGGGGGGAATTTCCTGTGTAGCGGTGAAATGCGTAGATATAGGAAGGAACACCAGTGGCGAAGGCGACCACCTGGACTGAAACTGACACTGAGGGGCGAAAGCGGGGGGAGCAAACG
-+
-AAAAABB?DDDDDDDDGFGFGGIIHHIIIIIHIIDFH>CFHHGDCFDH>CDHAEFEHIEFFGGHHHHHHHFH=CFFHHHHEHG8DEEGEGGGGGDEEEEGEEGGGCGGEEECCACCEGGGCEE::?CE0?CCEGE'.<'..4CEGEGGEEEE*::C>20>?C?*1:C..'8:??*:*?*0)??9CEG8?*1*8'4.44?58<28?C#############################################
-@MISEQ03:64:000000000-A2H3D:1:1101:12555:2129 1:N:0:TCCACAGGAGT
-TACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTCGTTAAGTTGGATGTGAAAGCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACGAGCTAGAGTATGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGTGAAATGCGTAGATATAGGAAGGAACACCAGTGGCGAAGGCGACCACCTGGACGGAAACTGACACTGAGGTGCGAAAGCGTGGGGACCAACCG
-+
-????ABBADDDDDEDDGGGGGGIIHHIIIIIHIIHHHFFHHHFHHHHH>CDHAEFHFGHHFHHHHHHHHHFHHFHFFHHHHHGBEEAD;DGGGGEGGGCGCEEEGEGGGCE>>>CEDGDGE:C:CGGG:?C??EE08<)0?ECEGEGCCECEEGGGGG08CECE?CE8)4?CC:*:*:0989*9CEC8C*:?C'842.8'.4.2?E9?*:?'.8).::::?CC:*110*0C8C<8??C#############
-@MISEQ03:64:000000000-A2H3D:1:1101:13627:2170 1:N:0:TCCACAGGAGT
-GACAGAGGGTGCAAACGTTGTTCGGAATTACTGGGCATAAAGAGCACGTAGGTGGTCTGCTAAGTCACGTGTGAAATCCCCCGGCTCAACCGGGGAATTGCGCGTGATACTGGCCGGCTCGAGGTGGGTAGGGGGGAGCGGAACTCCAGGGGGAGCGGGGAAATGCGTAGATATCTGGAGGAACACCGGGGGCGAAAGCGGCTCACGGGACCCAATCTGACACTGAGGGGCGAAAGCTAGGGTGGCAAACG
-+
-?????BB?DDDDDDDDEFFFFFHHHHHIHIIHIIFHCEHIIHBFHIHHAAFH5CF@FHHHGHIIGHHHHFHIHIIIHIIIHHHHHHHHHHFHHHFFEFEFEDBE<>BBEEFECECE?D'..2AD)8A>40?AED''''.4<D>>AC**1?).2'888D'5<EACEEEAEDEFEE:*??*08A?AAC)58'4>2<>D8A:A82'.*:*.'?>E)AA####################################
-@MISEQ03:64:000000000-A2H3D:1:1101:11781:2223 1:N:0:TCCACAGGAGT
-TACGTAGGGCGCAAGCGTTATCCGGAATTATTGGGCGTAAAGAGCTCGTAGGCGGTTTGTCGCGTCTGCCGTGAAAGTCCGGGGCTCAACTCCGGATCTGCGGTGGGTACGGGCAGACTAGAGTGATGTAGGGGAGATTGGAATTCCTGGTGTAGCGGGGAAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGGTCTCTGGGCATTAACTGACGCTGAGGAGCGAAAGCAGGGGGGGCGAACG
-+
-???A?BB?DDDDDDDDEEECFFHHHHHIHHHIIIHHHECEHFCFHGGH>CFEFEHHHHHFFDFHCDEFFHHEBFFFF?BBEEEEEEEFFFBEEEEAEDEFEDD.8A8.ACEDDD;AEFFFFEF:*1:?ACCFFD8<AE?EFFFF:EEEEFFFA:CEDD'.8??CEF?ADDDFF:C:?::?AEEFFFA>8'08:2448DE?E?8:*:*1A***0*:AA*?AEEEEE?#########################
-@MISEQ03:64:000000000-A2H3D:1:1101:17996:2254 1:N:0:TCCACAGGAGT
-TACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGTTAAGTTGGATGTGAAAGCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACAAGCTAGAGTATGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGGGAAATGCGTAGATATAGGAAGGAACACCAGGGGCGAAGGCGACCACCGGGCCTGAAACTGACACTGAGGGGGGAAAGCGGGGGGGGAAAACG
-+
-?????BB?DDDDDDDDGGGGGGIHHHHIIIIHHHFFH>CHFHGHHHEHCCCE5AFEHIHHHHHHHHHHHHHHHHHHHHHHHHGGEEGGEGEGGGEGEGGGCGGGGGGGECGEECGAECGGEEEC**CE?C::CCC.8<)08?CCC:CCCEC?CC?:8>'4<?.1C:8082CCGG*:*:0C8?EC*0C89.?############################################################
-@MISEQ03:64:000000000-A2H3D:1:1101:13712:2276 1:N:0:TCCACAGGAGT
-TACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGTTAAGTTGGATGTGAAAGCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACAAGCTAGAGTATGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGGGAAATGCGTAGATATAGGAAGGAACACCAGTGGCGAAGGCGACCACCTGGACTGATACTGACACTGAGGGGGGAAAGCGGGGGGGGAAAACG
-+
-?????BBADDDDDDDDGGEGGGIHHHHIIIIIIIIIHCCHHDCECHEHCDEH-AFEHIHIHHIHHHHHHHHHHHFFFHHHHHGEGEDDEEDDDGGGGGEGGGGGEEEGEEGEGGGGGGGCEGEGCEGG:C::CEE)88.8?EGGG:C?:?:C??:*52'.888:CEE).2CCGE*C??:C.?EGGGGC9*118>>.4>C''.8<CC*?*:**00*01?:CEGCC###########################
-@MISEQ03:64:000000000-A2H3D:1:1101:15819:2301 1:N:0:TCCACAGGAGT
-TACGTAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTGAGTTAAGTCTGCTGTGAAAGCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACAAGCTAGAGTATGGTAGAGGGTGGGGGAATTTCCTGTGTAGCGGGGAAATGCGTAGATATAGGAAGGAACACCAGGGGCGAAGGCGACCACCTGGACTGAAACTGACACTGAGGGGCGAAAGCGGGGGGGGCAAACG
-+
-?????BB?DEDDDDDDFDEEFFHHHEFHHIIIIIIHHCHHFHHHCEEACCHHHEH)<<CCDGFFDFFFBCB@DFHFHFHHEEFB8@EEEFFEEFFFFFFFFFEFCEFFFCAAC?EF??AC???0*:?C*:::?EE)0>'.42AAECEFE:*0:AAC?D'..8C?:?A)).0001*11::??8A**?A################################################################
-@MISEQ03:64:000000000-A2H3D:1:1101:11958:2304 1:N:0:TCCACAGGAGT
-TACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGTTAAGTTGGATGTGAAAGCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACAAGCTAGAGTATGGTAGAGGGTGGGGGAATTTCCTGTGTAGCGGGGAAATGCGTAGATATAGGAAGGAACACCAGGGGCGAAGGCGACCACCGGGACTGAAACTGACACTGAGGGGCGAAAGCGTGGGGGGCAAACG
-+
-????ABBADDDDDDDDEEEEFFHHHHHIFHHIIIHFEECEFGDECECE5>C:55EEHIHIFGHFGHHHHHFHFFHHFHHHHHFBFEEDEEFFFFEFFFEFEFABEEFFFEEBEFFEFF=::AE*:AEE0?:?CFE8A>'.<?EEE??E?A??CEEF<>'.8AC?ECE)848?0**::AAC???EEE)*0)084'48<'8'882<CA).2<408?*1:??EEE#############################
-@MISEQ03:64:000000000-A2H3D:1:1101:19110:2311 1:N:0:TCCACAGGAGT
-TACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGTTAAGTTGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACAAGCTAGAGTATGGTAGAGGGGGGTGGAATTTCCTGTGTAGCGGTGAAATGCGTAGATATAGGAAGGAACACCAGTGGCGAAGGCGACCACCTGGACTAAAACTGACACTGAGGGGCGAAAGCGGGGGGGGCAAACG
-+
-????9BB?BBBBBBBBEEECFAFHHHHHHHFHHHHHHCCEFF/CDCCE>DCH5AECFHHHFHHHHHHHHHHHGFHHCFHHHHHEEEDEDEED@EEEEEEEEEEEEEEEEE;;BEEE?EEEEEE?*?CA?EE::?8'.''..?CEE*::/:?A:C?E??82?CCEEEE))4?EEEEA:?*80?AEEC#################################################################
-"""
-
-# For reference. Data used to make the 'joined_reads' reference string.
-reverse_reads = """@MISEQ03:64:000000000-A2H3D:1:1101:14358:1530 2:N:0:TCCACAGGAGT
-ACGGACTACAAGGGTTTCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGTGTCAGTATCAGTCCAGGTGGTCGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCATACTCTAGCTTGTCAGTTTTGAATGCAGTTCCCAGGTTGAGCCCGGGGATTTCACATCCAACTTAACAACCCACATACCCGCCTTTTCGCCCAGGTAATCC
-+
-?????@@BDDBDDDBBCFFCFFHIIIIIIIIFGHHHHEHHHIIIHHHHHFHIIHIGHHIDGGHHHHIIIIICEFHIHHCDEHHHHHHFHHCFHDF?FHHFHHHFFDFFFDEDDD..=DDDE@<BFEEFCFFCECE==CACFE?*0:*CCAA?:*:*:0*A?A80:???A?*00:**0*1*:C??C?A?01*0?);>>'.8::A?###############################################
-@MISEQ03:64:000000000-A2H3D:1:1101:14206:1564 2:N:0:TCCACAGGAGT
-ACGGACTACAGGGGTTTCTAATCCTGTTTGCTCCCCACGCTTTCGTGCATGAGCGTCAGTGTTAACCCAGGGGGCTGCCTTCGCCATTGGTATTCCTCCACATCTCTACGCATTTCACTGCTACACGTGGAATTCTACCCCCCTCTGCTACACTCTAGCCTTGTAGTTTCAAACGCAGTTCCCAGGTTGAGCCCGGGGCTTTCACATCTGCCTTACAAAACCGCCTGCGCACGCTTTACGCCCCGTAATTC
-+
-?????@@BDDBDDD?@CFFFFFHHHHHFFHHHHHHHHHHH@FFHEDFFH@FHBGCDHHHBFHHHHHHHEHHHHDCCEFFDFFFEE:=?FF?DFDFDFFF==BEE=DBDDEEEEEB,4??EE@EEE,3,3*3,?:?*0ACCEDD88:***?*0:*0***0*?C?00:AE:?EE:*A8'.?:CAA?A80*0*??AA88;28;C##################################################
-@MISEQ03:64:000000000-A2H3D:1:1101:14943:1619 2:N:0:TCCACAGGAGT
-ACGGACTACAGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGTGTCAGTATCAGTCCAGGTGGTCGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCATACTCTAGCTTGTCAGTTTTGAATGCAGTTCCAAGGTTGAGCCCGGGGCTTTCACATCCAACTTACAAAACCACCTACCCGACCTTTACGCCCAGAAATTC
-+
-?????@@BDDDDDD?AFFFFFFIIHHIHIIHIIIIHIHHHHHHHHHHHHHHHHHHIHHHIIHHIHIIIIII?EFEGHHHHHIIHHDHHFD@FFEHFHFHFHFHFFFFFFFFEEEEFFFDEB<E@EFEEABA=B=CAEFEEFEA?A:*AC::??:**10??:00::*??EC*?:?C*::A*?C*1:8A################################################################
-@MISEQ03:64:000000000-A2H3D:1:1101:15764:1660 2:N:0:TCCACAGGAGT
-ACGGACTACCGGGGTATCTAATCCTGTTTGCTCCCCTAGCTTTCGCACCTCAGCGTCAGTACCGGGCCAGTGAGCCGCCTTCGCCACTGGTGTTCTTGCGAATATCTACGAATTTCACCTCTACACTCGCAGTTCCACTCACCTCTCCCGGACTCAAGACCGCCAGTACCAAAGGCAGTTCTGGAGTTGAGCTCCAGGTTTTCACCCCTGCTTTAAAAATCCCCCAACGCGGCCTTTCCCCCCAGTGACTC
-+
-?????@=BB?BBBB<?>ACFFCECFCHCFHH=CGHHDFH=E?ACDEHHCCFFGHHDHH@CBEFHHCHHHF,5@?DF)4<C3D4DD+=,BD5;DE=DBDE=<E<;?E?B;3?;A?;;;EBBC:??EEEEE?;AA*:A??#################################################################################################################
-@MISEQ03:64:000000000-A2H3D:1:1101:15211:1752 2:N:0:TCCACAGGAGT
-ACGGACTACCGGGGTTTCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGTGTCAGTATCAGTCCAGGTGGTCGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCATACTCTAGCTTGTCAGTTTTGAATGCAGTTCCCAGGTTGAGCCCGGGGATTTCCCATACAACTTAACAAACCACTTACGCGGGTTTTCGCCCCACAAATTC
-+
-?????@@BB-<@BBBBEA?FFFA8ACFCBHHHGHHHHBHHHHFCDDD7CHHFE?CCDDCFGBHHHGGHFGFGFFHFDCDHHC?=CDHFFDCDDDF,EFF5?BFEDBBDB@@EEACCE;,?::@BEEEEACC*??//:AA*8AAAEE?ECC#####################################################################################################
-@MISEQ03:64:000000000-A2H3D:1:1101:15201:1774 2:N:0:TCCACAGGAGT
-ACGGACTACCGGGGTTTCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGTGTCAGTATCAGTCCAGGTGGTCGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCATACTCTAGCTTGTCAGTTTTGAATGCAGTTCCCAGGTTAAGCCCGGGGATTTCCAATCCAACTAAACAAAACACACACCCGCTCTTTACGCCCACCATTTC
-+
-?????@=BBBBBBB<=CFFFFFFHFCFCEHHDGHHEFEHHHHHHHHHHHFHHGC-AEGFCGHHHFFHFHHBFGDEDDCEDDH+DDDHHF,,7D@DFDFFFBFFEDEDEEDE:@:B?C;,3@<><EEEE*BEEC?E*0AEEEEE*8*:CCE:CA*?*A?:AAA#########################################################################################
-@MISEQ03:64:000000000-A2H3D:1:1101:15976:1791 2:N:0:TCCACAGGAGT
-ACGGACTACAAGGGTTTCTAATCCCGTTTGCTCCCCTAGCTTTCGCACCTCAGCGTCAGAAATGGACCAGAGAGCCGCCTTCGCCACCGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCATACTCTAGCTTGTCAGTTTTGAATGCAGTTCCCAGGTTGAGCCCGGGGTTTTCCAATCCAATTTAACGACCAACCACGCGGCGCTTTAGGCCCGGTAATGC
-+
-?<???@=BBBBBBB556CFFBCEFFEHHHHHHHHHE=EHHHHHHHHHHHHHHHFHHEDCGFHHHHHHHHH;A?EFHHHHHHHHH+=EHHC)8@+?BFFFDFEEEEE;DDEEEEBCEECEEEBEEEEEEEEEEE:?*/:ACEE)*8*:C:A*0?:A*:C?A:?**:AECE?*?:*:C:????C#####################################################################
-@MISEQ03:64:000000000-A2H3D:1:1101:16031:1840 2:N:0:TCCACAGGAGT
-ACGGACTACTGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGTGTCAGTATCAGTCCAGGTGGTCGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTTAACAATACTCTAGCTTGTCAGTTTTAAATGCAGTCCCCAGGTTGAGCCCGGGGCTTTCACATCAAATTTACAAAACCACCCACGCGCGTTCTACGCCGGACAATCC
-+
-?????==<BBBBBBBBFFFFF?FFF?FFFHHFEFFHHHH:@>CHEDHHHFFFGBCCDDFGGHHHHEHHHHH5AE+C*>==+EDHHDEFCFCDF3@.D=,CFH=,@,4DFFE:=DDDDEB:)1:1;;?B;BE;??,?EE;AEE??**0*/:0??:***:?E*:8?A*:CEE#################################################################################
-@MISEQ03:64:000000000-A2H3D:1:1101:12964:1852 2:N:0:TCCACAGGAGT
-ACGGACTACTCGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGTGTCAGTATCAGTCCAGGTGGTCGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCAACCACCCTCTACCATACTCTAGCTTGTAAGTTTTGAATGCAGTTCCAAGGTTGAGCCCGGGGCTTTCACACCCAACTTAACAACCCACCTACGCGGCATTTACGCCCACTACTTC
-+
-?????@=BBBB9?=55AACCC?ECFFFHB>FFHGFHFHHHHHHHHHHHHFHHHGGGHHHGGHHHHHHDDFEGH;EBCEHD+AFE@C+@F=.7D+@CDCFFHHFFFD?DF@E+=:BDDB;D=@BE?BCE*,33,,?,3;;:?).0**::***0/*/0A??:*:****00/**8*0?AE:?AAC**0):??C#############################################################
-@MISEQ03:64:000000000-A2H3D:1:1101:17245:1906 2:N:0:TCCACAGGAGT
-ACGGACTACAGGGGTTTCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGTGTCAGTATCAGTCCAGGTGGTCGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCATACTCTAGCTTGTCAGTTTTGAATGCAGTTCCCAGGTTGAGCCCGGGGCTTTCAAATCCAACTTAACAAACAACCAACCGGCGCTTTACGCCCAGTAATTC
-+
-?????@@BDDDDBDABEFFFFFHHHHHHHHGGHGHHHHHHEH@FEHEEHHHFHHH=EGHHHHDGHHHHFHHGGHHHCCEDEHHHHHHHHHDFHHF=DBDFHFD?BB.BF;@DDDD.=DD*>6)@==ABAACBB5=B,=,88A)???:E*::::??*:**1**8??CCCEE8A:A::AAACAC??A)1:0**1*)48;'42A?EA**1?*1*0::??:ACEF##############################
-@MISEQ03:64:000000000-A2H3D:1:1101:18171:1983 2:N:0:TCCACAGGAGT
-ACGGACTACCGGGGTTTCTAATCCTGTTCGCTCCCCACGCTTTCGCGCCTGAGCGTCAGGTAAGGCCCAGAGATCCGCCTTCGCCACCGGTGTTCCTCCTGATATCTGCGCATTTCACCGCTACACCAGGAATTCCGATCTCCCCTACATACCTCTAGCCGGGCAGTATCGGATGCAGACCCGAGGTTGAGCCCCGGGATTTCACATCGGCTTACCAAAGCGCCCGGCGCCCCCTTTACGCCCCAGAAACC
-+
-?????@@BDBDDDD=BCFFFFFIIIIHHFEHHHHIHIHHHEFCGDEHHHEFFEGC>EEHI?EHHGHHHHFH+C=,,?FHDDHFEE@EFE=1;A;EECCE==BEB,BBC=@@<?EE:?E:8>24;:CEAA8?CC*??:0?;*1?AE?CE*10:0*1:CAA*;22;2A#####################################################################################
-@MISEQ03:64:000000000-A2H3D:1:1101:14225:2009 2:N:0:TCCACAGGAGT
-ACGGACTACAGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGTGTCAGTATCAGTCCAGGTGGTCGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCATACTCTAGCTTGTCAGTTTTGAATGCAGTTCCCAGGTTGAGCCCGGGGCTTTCACATCCAACTTAACAAACAACCACGCCGCGCTTTAGCCCAGGTAATTC
-+
-?????@@BDDDDDD??CFFFFFHIHHHHIIIIHIIHIHHHHHIHHHHHHFFHHIHHHIHHHHHIIHIHIIIFFFEGHHEDEHHHHDHHHHCFFDFFHHHHHHFFFFFFF@EDEED=DDEED@EBFCEEEFECCCEEEFB<CA888:AEEFEFEA??CCEFF:?:ACCFFE?E:AC?:*:?EFE*:):???::A).;D>D>8:?################################################
-@MISEQ03:64:000000000-A2H3D:1:1101:16656:2052 2:N:0:TCCACAGGAGT
-ACGGACTACCCGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGTGTCAGTATCAGTCCAGGTGGTCGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCCCCCTCTACCATACTCTAGCTTGTCAGTTTTGAATGCAGTTCCAAGGTTGAGCCCGGGGCTTTCACACCCAACTTAACAAACCACCTACGCGCGCTTTACGCCCAGCATTTC
-+
-?????@@BDDDDDD<@CFFFFFIHHFHHFHHHHHHHIHHHHHFHCEHHHHIIFHHAFHHHFFHIIHHIIIHGHFEH<DDEDH;DEHHHHHFFH;FFHFHFFFFD?FBFF=BDEDDDFEEAE@BEFFFF<BE=B,=,5?*).;>8A:*:::?E?*::A::?AE8AEFEEEC?A:CE?AEA:EF*008:?EF*:C)8;D228A0:??:*.8A8):*:*1::CE##############################
-@MISEQ03:64:000000000-A2H3D:1:1101:18209:2060 2:N:0:TCCACAGGAGT
-ACGGACTACTAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGCGTCAATACTTGTCCAGCGAGTCCCCTTCGCCACTGGTGTTCTTCGGAATATCTACGAATTTCACCTCTACACCCGGAATTCCACTCCCCCTTCCAAGATTCCAGCTTAGCAGTTTCAAGGGCAGTTCCGGGGTTGGCACCCGGGATTTCACCCCTGCCTTGCTCAACCCCCCACGGGGCCTTTACCCCCAGCATTCC
-+
-=9<=9<7<@@@@@@<@A8A>C>8E>-8AE;C99CEEECC>>EECE@CCDE,C@E++5>E-A=E-C@@=@5@C>C<D-5A5CC<CD+<4DE3=<C+4==+<@D++2:9DEE1<9DE########################################################################################################################################
-@MISEQ03:64:000000000-A2H3D:1:1101:13824:2095 2:N:0:TCCACAGGAGT
-ACGGACTACCAGGGTTTCTAATCCTGTTTGCTCCCCACGCTTTCGCGTCTCAGCGTCAGTAACGTCCCAGCGAGCTGCCTTCGCAATGGGTGTTCCTCCTGATATCTGCGCATTTCACCGCTACACCAGGAATTCCACTCCCCCCTTCCGTACCCTAGCCCGACAGTACCCCCCGGCTTCCGAGGCTTGACCCCCCGCCTTTCACACCGGACTTACCGGGCCGCCTACCCGGCCTTTCGCCCCACCGTTTC
-+
-??<??@@BBBBBBBBBCFCFFFHHHHHHBHHGHHHHHCHHEH>GDEHCA:DFGHHEEEEFFHHHHHHDHED7<CHEGHFFDFFHEDHHHDDDE@D??DD;=B,,5B,,56)):?;BEE?*1::):?**8AEAC*?*:?#################################################################################################################
-@MISEQ03:64:000000000-A2H3D:1:1101:17839:2106 2:N:0:TCCACAGGAGT
-ACGGACTACAAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGTGTCAGTATCAGTCCAGGTGGTCGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCATACTCTAGCTTGTCAGTTTTGAATGAAGTTCCAAGTTTGAGCCCGGGGCTTTCACATCCAATTTAAAAAACAACCAACGCGCGCTTCACCCCAGGTAATAC
-+
-?????@@BBBBBBB<5ACFFFFHHHHHHHHHHHHHHHHHHHHFFHHHHHHHHHGHHHFHGHHHHFGHHHHH?EFEECCEEEHHHEHHHHHDFHDFDHDHHHHFFDFFFHFEDDDD,5DD@BB<EEEEECBB?B3B;,?,3?E8CE?*?A*/:/:::??AE::**0:AEE##################################################################################
-@MISEQ03:64:000000000-A2H3D:1:1101:17831:2124 2:N:0:TCCACAGGAGT
-ACGGACTACAAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGTGTCAGTATCAGTCCAGGTGGTCGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCATACTCTAGCTTGTCAGTTTCGAATGCAGTTCCCAGGTTGAGCCCGGGCCTTCAACCTCCACTTTACAAAACAACCAAACGCCGCTTACCGCCACGAAATCC
-+
-?????@=BBBBBBB5<CFFFFCFHHHHHFHHHHHHHHHHHHHFHEEHHEHFGHGHFGDF?EEFHHHHDGHH=EHEGCCEEEHHHHHH@FFCFH+CFHCFHHHHHFFFHHFE:DDD,=EBDEBE<EEEE?;B?B?E?CEEEEEE8A?CC#######################################################################################################
-@MISEQ03:64:000000000-A2H3D:1:1101:12555:2129 2:N:0:TCCACAGGAGT
-ACGGACTACCGGGGTTTCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGTGTCAGTATCAGTCCAGGTGGTCGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCATACTCTAGCCCGTCAGTTTTGAATGCATTTCCCAGGTTGAGCCCGGGGCTTTCAAACCCAACTAAACAAACAACCAACGCGCGTTTTCCGCCACGTAATTC
-+
-?????@@BDDDDDDDDEFFFFFHHHFHIIIHHHIIHHHHHEHFHEHHHHIFGHHIHIHFHI=FHFIHIIIHDFHHHHEHEDHHHHHHHHHHHH@FBFFFFFFFEFDEFE6@:@ACBEFFEEB@BCB=A<<A?C:A::C8AEE)0?A*?A:*:**10?1**1.4A88?EE?#################################################################################
-@MISEQ03:64:000000000-A2H3D:1:1101:13627:2170 2:N:0:TCCACAGGAGT
-ACGGACTACTAGGGTATCTAATCCCGTTTGCTACCCTAGCTTTCGCACCTCAGTGTCAGATTGGGTCCAGTGAGCCGCTTTCGCCACCGGTGTTCCTCCAGATATCTACGCATTTCACCGCTCCACCTGGAGTTCCGCTCACCCCTACCCACCTCGAGCCGGCCAGTATCCCGCGCAATTCCCCGTTTGAGCCGGGGGTTTTCCCAAGGGTCTTAACAGCCCACCTACGTCCCCTTTATGCCAGGTAATTC
-+
-?????@=BD?BBDD?58ACFFCHHHHHHHHFGHHHEEFHHHHHCDEEEECFDGFHDGHHHHFFFHEHHHHHHHFFFHAEHFFEHHHHFHH<DE:C--@F-CCF=,,4BDFE:@E,BBED@:)2>=C?;BC=?C,==*3.84?EC?88A8A:A?*8?###############################################################################################
-@MISEQ03:64:000000000-A2H3D:1:1101:11781:2223 2:N:0:TCCACAGGAGT
-ACGGACTACTGGGGTATCTAATCCTGTTCGCTCCCCATGCTTTCGCTCCTCAGCGTCAGTTAATGCCCAGAGACCTGCCTTCGCCATCGGTGTTCCTCCTGATATCTGCGCATTTCACCGCTACACCAGGAATTCCAATCTCCCCTACATCACTCTAGTCTGCCCGTACCCACCGCAGATCCGGAGTTGAGCCCCGGACTTTCACGGCAGACGCGCAAACCGCCCACAGAGCTCTTTCCCCCCAAAAATCC
-+
-?????@@BDDDDDDBDCFFFFFHHHHHHHHHHHEHEHDFHHHHHHEDEEHHHFHHHHEHHHHHFGHHHHDD;EFFHCFECAGFEEE+@E@3?E:DFFFHBDHC?BBDFFE8;=DD,,=DEE<@),==?B*44=,=,4**0*0:CA*A?::*0::?0AC:CE*?:*8.4AE?*8?)'82;*?0?####################################################################
-@MISEQ03:64:000000000-A2H3D:1:1101:17996:2254 2:N:0:TCCACAGGAGT
-ACGGACTACCAGGGTTTCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGTGTCAGTATCAGTCCAGGTGGTCGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCATACTCTAGCTTGTCAGTTTTGAATGCAGTTCCCAGGTGGAGCCCGGGGCTTTACAATCAAACTTAACAAACCCCCTACGCGCGCTTTAGCCCCACAATTTC
-+
-?9???@@BBDDDDD<BEFFFFFHHHHCEFHGGHHHHHAEHEHFHEEHHCBFHFFHEGHFCGGFCGHHFHHFGHHHHDHHECEDEHDDHH?@?FDFDHHHFHFFDDHDFFFEEEEEDEDB=>BBEE=BECEEEE,B=?CBACE)*0**?C?*:*0:*:?:A:??**::?E**80::::??:CAC:C8C################################################################
-@MISEQ03:64:000000000-A2H3D:1:1101:13712:2276 2:N:0:TCCACAGGAGT
-ACGGACTACTGGGGTTTCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGTGTCAGTATCAGTCCAGGTGGTCGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCATACTCTAGCTTGTCAGTTTTGAATGAAGTTCCAAGGTTAAGCCGGGGGCTTTCACATCCAACTAACCAAACCACTAACCGCCGCTTTAGGCCCAGCAATTC
-+
-?????@@BDDDDDDBDEFFFFFHFHHHIFFHIHIIHHEHHHHFHHHEHCFHHDFGGHIIHIHFGHHHGFHF-AEEGHHHHEGFHHHDFHB?FHEHCF?FDDFH??BFFFF=DDEEEFFEDE8>:BECCAEEAECE,ABAACEA*0**?*01?001*::*A**0:*::CE1*8:?**11:*CE#####################################################################
-@MISEQ03:64:000000000-A2H3D:1:1101:15819:2301 2:N:0:TCCACAGGAGT
-ACGGACTACCGGGGTTTCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGTGTCAGTATCAGTCCAGGTGGTCGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCATACTCTAGCTTGTCAGTTTTGAATGAAGTTCCCAGGTTGACCCCGGGGCTTTCACAGCAGCCTTAACTCACCCCCTGCCAACCCTTTACTCCCCGAAATTC
-+
-?9???@=BDDDDDD<@CFFFFFHHHBFFHHHFGHHHHHHHEHFGEHHHHEDGD?FCGHHFHHHHHHHHBDF?FHHHFHH@DHHHH+DHHDCFHDFDFBFFDFFEDFEEDEEDEEC=CCEEEBEEFCEFEEFEE?:CEE*8CA800*:E*:AA::***1??*:**1::CF##################################################################################
-@MISEQ03:64:000000000-A2H3D:1:1101:11958:2304 2:N:0:TCCACAGGAGT
-ACGGACTACTGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGTGTCAGTATCAGTCCAGGTGGTCGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCATACTCTAGCTTGTCAGTTTTGAATGCAGTTCCCAGGTTGAGCCCGGGCCTTTAAAATCCAACTTAAAAAACAACTAACCGCCGCTTTCCGCCCAGAAATCC
-+
-?????@@BDBDDD@@BFFFFFFHFHHHHFHHHHHHHHHHHHHHHHHHHHHFHHHHHFGH=CGEH=FHFGHFEFHEHHCEEEHHHDCEFHH.?FDFFHHHHBFHFFHFFFFEEEEEEEEEEB@EEEECE;CC?BCEEEC;;CEA*8:AE**00::C0A::?:*0*AEE?E?*A**:C?*:?:?**0)00::**?8>'8';ACA*0*0C?:?******::??E?CE###########################
-@MISEQ03:64:000000000-A2H3D:1:1101:19110:2311 2:N:0:TCCACAGGAGT
-ACGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGTGTCAGTATCAGTCCAGGGGGTCGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCATACTCTAGCTTGTCAGTTTTGAATGCAGTTCCCAGGTTAAGCCCGGGGCTTTCCAACCCAACTTAACAAACCACCTACCCCCGCTTTACGCCCAGAAATTC
-+
-?????@=BDDDDDD<5CFFFFFHHHHHF>CGFHHHHHHHEEHFHEHHHHHHHGAFGHHHHH-5AF5AFHHD+5*5CCCDDHFFHEEHFHHBFF:BDD4?=.=DEFFEBEDEBEEECEFFEE<::CEAACE?:A*1:*C88?AE.?:*::**1:**11*01***1?C??:?0?:C:C**1*1::*:8A?10*1?##########################################################
-"""
-
-joined_reads = """@MISEQ03:64:000000000-A2H3D:1:1101:14358:1530 1:N:0:TCCACAGGAGT
-TNCAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGTTAAGTTGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACAAGCTAGAGTATGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGTGAAATGCGTAGATATAGGAAGGAACACCAGTGGCGAAGGCGACCACCTGGACTGATACTGACACTGAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGAAACCCTTGTAGTCCGT
-+
-?#5<????DDDDDDDDEEEEFFHHHHHHHHHHHHHHDCCHHFGDEHEH>CCE5AEEHHHHHHHHHHHHHHHHHFFFFHHHHHHEEADEEEEEEEEEEEEEEEEEEEEEEE?BEEEEEEEEEEEAEEEE0?A:?EFCAC==ECEEFFEFEEFBACEEDD=8CDDDEDFFFDFFHHHFHHFAFDHFCHHFHHHHHHEDCHHIHFECIIIIIHHHHGGDIHHGIHIIHFHHHHHIIIHHHEHHHHGFIIIIIIIIHFFCFFCBBDDDBDDB@@?????
-@MISEQ03:64:000000000-A2H3D:1:1101:14206:1564 1:N:0:TCCACAGGAGT
-TACGTAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTTTTGTAAGTCAGATGTGAAAGCCCCGGGCTCAACCTGGGAACTGCGTTTGAAACTACAAGGCTAGAGTGTAGCAGAGGGGGGTAGAATTCCACGTGTAGCAGTGAAATGCGTAGAGATGTGGAGGAATACCAATGGCGAAGGCAGCCCCCTGGGTTAACACTGACGCTCATGCACGAAAGCGTGGGGAGCAAACAGGATTAGAAACCCCTGTAGTCCGT
-+
-?????BB?DDDDDD@DDCEEFFH>EEFHHHHHHGHHHCEEFFDC5EECCCCCCDECEHF;?DFDDFHDDBBDF?CFDCCFEAA@?:;EEEEEEEECBA,BBE?EEAAECA0:?C?:??A:8*:00?0**:8:DDECDD0.?:????:,:?EEEEEE??44BEEEEEDDBD=EEB==FFFDFDFD?FFEE:EEFFFDFFECCDHHHHEHHHHHHHFBHHHDCGBHF@HFFDEHFF@HHHHHHHHHHHFFHHHHHFFFFFC@?DDDBDDB@@?????
-@MISEQ03:64:000000000-A2H3D:1:1101:14943:1619 1:N:0:TCCACAGGAGT
-TACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGTTAAGTTGGATGTGAAAGCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACAAGCTAGAGTATGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGTGAAATGCGTAGATATAGGAAGGAACACCAGTGGCGAAGGCGACCACCTGGACTGATACTGACACTGAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCCTGTAGTCCGT
-+
-?AAAABBADDDEDEDDGGGGGGIIHHHIIIIIIIHHHCCHHFFEFHHHDCDH5CFHIIHIIIIHHHHHHHHHHHHHHHHHHHGGGEGGGGDDEGEGGGGGGGGGGGGGGEEEGCCGGGGGGEGCEEEECEAECGFEEFEACEEGGGEEEFECE<BEDFFFEEEEFFFFFFFFHFHFHFHFHEFFCEFHHDHHIIHHHHHGEFE?IIIIIIHIHHIIHHHIHHHHHHHHHHHHHHHHHHIHIIIIHIIHIHHIIFFFFFFA?DDDDDDB@@?????
-@MISEQ03:64:000000000-A2H3D:1:1101:15764:1660 1:N:0:TCCACAGGAGT
-TACGAAGGGGGCTAGCGTTGCTCGGAATCACTGGGCGTAAAGCGCACGTAGGCGGATTGTTAAGTCAGGGGTGAAATCCTGGAGCTCAACTCCAGAACTGCCTTTGATACTGGCGATCTTGAGTCCGGGAGAGGTGAGTGGAACTGCGAGTGTAGAGGTGAAATTCGTAGATATTCGCAAGAACACCAGTGGCGAAGGCGGCTCACTGGCCCGGTACTGACGCTGAGGTGCGAAAGCTAGGGGAGCAAACAGGATTAGATACCCCGGTAGTCCGT
-+
-???????@DDDDDDBDFEEFEFHEHHHHHHHHHHHHHEHHHHFEHHHHAEFHGEHAHHHHHHHHHHHHHHH=@FEFEEFEFEDAEEEFFE=CEBCFFFCECEFEFFFCEEEFFCD>>FFFEFF*?EED;?8AEE08*A?A:?EA;?EEEEE??:CBBE?EEEFEEE?BCE?;CE?=EDEE=EECEFE?C0DD8D4C<DEFD?@5,FHHHCHHFEBC@HHDHHGFFCCHHEDCA?E=HFDHHGC=HHFCHCFCECFFCA>?<BBBB?BB=@?????
-@MISEQ03:64:000000000-A2H3D:1:1101:15201:1774 1:N:0:TCCACAGGAGT
-TACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGTTAAGTTGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACAAGCTAGAGTATGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGTGAAATGCGTAGATATAGGAAGGAACACCAGTGGCGAAGGCGACCACCTGGACTGATACTGACACTGAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGAAACCCCGGTAGTCCGT
-+
-?????BB?DDDDDDBDEEEEFFHFHHHHHHHHHHHFH>CEHDGDDCDE5CCEACFHHHHHHHHFFHHHHHHHHFHHFHHHHHHDEBFEEE@DEEEEEEEEEEEEEEBBCBECEEEEEEEEEEEEEEECACCEEEEEEA00E?EEEBAEEEE?>?CEDDC?B?A:EDEEDEDEFFBFFFDFD@DEEEFHHDDD+HDDECDDEDGFBHHFHFFHHHGCFGEEEEGHHFHHHHHHHHHHHEFEHHGDHHECFCFHFFFFFFC=<BBBBBBB=@?????
-@MISEQ03:64:000000000-A2H3D:1:1101:14225:2009 1:N:0:TCCACAGGAGT
-TACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGTTAAGTTGGATGTGAAAGCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACAAGCTAGAGTATGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGTGAAATGCGTAGATATAGGAAGGAACACCAGTGGCGAAGGCGACCACCTGGACTGATACTGACACTGAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCCTGTAGTCCGT
-+
-?????BB?DDDDDDBDEEEEFFHHHHIIIIHHIIIIHHEHIFGEHHHHCCEHAEFHIIHIIIIHHHHHHHHHHFHHHHHHHHFFFEFFFFFEFFFFFFEFFFFFFEFFFEFCACFFFFFFFAEFEFEEA?:AAEE<BFEEECCEFFEEEEFEEEFEEDD=DEEDEEFFFFFFFHHHHHHFFDFFFHHHHDHHHHEDEHHGEFFFIIIHIHIIHHHHHIHHHIHHFFHHHHHHIHHHHHIHIIHIIIIHHHHIHFFFFFC??DDDDDDB@@?????
-@MISEQ03:64:000000000-A2H3D:1:1101:16656:2052 1:N:0:TCCACAGGAGT
-TACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGTTAAGTTGGATGTGAAAGCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACAAGCTAGAGTATGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGTGAAATGCGTAGATATAGGAAGGAACACCAGTGGCGAAGGCGACCACCTGGACTGATACTGACACTGAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCGGGTAGTCCGT
-+
-?????BB?BDDDDDDDGFFEGGIIHHIIIIIHHHHIHCCFFDEEEHEHFFEH5AFHHIHIHIHGGHHHHHHHFHHFHHHHHHGEGFEGEGGEGGGGCEGGEGGGGEGGEFECGGGGGGGGEGGECEGG?CCCEGC08?50=?EGGBEFFFFEB@EAEEFDDDEDBCFFBF?DFFFFHFHFF;HFFHHHHHED;HDEDD<HEFHGHIIIHHIIHFFHHHFAHHFIIHHHHECHFHHHHHIHHHHHHHFHHFHHIFFFFFC@<DDDDDDB@@?????
-@MISEQ03:64:000000000-A2H3D:1:1101:12555:2129 1:N:0:TCCACAGGAGT
-TACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTCGTTAAGTTGGATGTGAAAGCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACGAGCTAGAGTATGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGTGAAATGCGTAGATATAGGAAGGAACACCAGTGGCGAAGGCGACCACCTGGACTGATACTGACACTGAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGAAACCCCGGTAGTCCGT
-+
-????ABBADDDDDEDDGGGGGGIIHHIIIIIHIIHHHFFHHHFHHHHH>CDHAEFHFGHHFHHHHHHHHHFHHFHFFHHHHHGBEEAD;DGGGGEGGGCGCEEEGEGGGCEA>>CEDGDGE:C:CGGG:AC??EEA8C::AECEGEGCCECEEGGGGGEBCECE@CEFEDFEFFFFFFFBF@HHHHHHHHHHHHDEHEHHHHFDHIIIHIFHF=IHFHIHIHHGFIHHHHEHFHEHHHHHIIHHHIIIHFHHHFFFFFEDDDDDDDDB@@?????
-@MISEQ03:64:000000000-A2H3D:1:1101:11781:2223 1:N:0:TCCACAGGAGT
-TACGTAGGGCGCAAGCGTTATCCGGAATTATTGGGCGTAAAGAGCTCGTAGGCGGTTTGTCGCGTCTGCCGTGAAAGTCCGGGGCTCAACTCCGGATCTGCGGTGGGTACGGGCAGACTAGAGTGATGTAGGGGAGATTGGAATTCCTGGTGTAGCGGTGAAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGGTCTCTGGGCATTAACTGACGCTGAGGAGCGAAAGCATGGGGAGCGAACAGGATTAGATACCCCAGTAGTCCGT
-+
-???A?BB?DDDDDDDDEEECFFHHHHHIHHHIIIHHHECEHFCFHGGH>CFEFEHHHHHFFDFHCDEFFHHEBFFFF?BBEEEEEEEFFFBEEEEAEDEFEDD.?EA4ACEDDDECEFFFFEF:*::?ACCFFD8<AE?EFFFF:EEEEFFFA<EEDD,.DD?CEFFFDDDFFHDBHFFFDEEFFFE@8EEEFGACEFEHFFE;DDHHHHGFHHHHHEHHHHFHHHEEDEHHHHHHFDHEHEHHHHHHHHHHHFFFFFCDBDDDDDDB@@?????
-@MISEQ03:64:000000000-A2H3D:1:1101:15819:2301 1:N:0:TCCACAGGAGT
-TACGTAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTGAGTTAAGTCTGCTGTGAAAGCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACAAGCTAGAGTATGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGTGAAATGCGTAGATATAGGAAGGAACACCAGTGGCGAAGGCGACCACCTGGACTGATACTGACACTGAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGAAACCCCGGTAGTCCGT
-+
-?????BB?DEDDDDDDFDEEFFHHHEFHHIIIIIIHHCHHFHHHCEEACCHHHEH)<<CCDGFFDFFFBCB@DFHFHFHHEEFB8@EEEFFEEFFFFFFFFFEFCEFFFCAAC?EF??AC???AA:?E::::?EE80EEC:?EEFEEFECFEEBEEEDC=CEEDEEDEEFDEFFDFFBFDFDHFCDHHD+HHHHD@HHFHHHF?FDBHHHHHHHHFHHGCF?DGDEHHHHEGFHEHHHHHHHGFHHHFFBHHHFFFFFC@<DDDDDDB=@???9?
-@MISEQ03:64:000000000-A2H3D:1:1101:19110:2311 1:N:0:TCCACAGGAGT
-TACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGTTAAGTTGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCAAAACTGACAAGCTAGAGTATGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGTGAAATGCGTAGATATAGGAAGGAACACCAGTGGCGAAGGCGACCCCCTGGACTGATACTGACACTGAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCGT
-+
-????9BB?BBBBBBBBEEECFAFHHHHHHHFHHHHHHCCEFF/CDCCE>DCH5AECFHHHFHHHHHHHHHHHGFHHCFHHHHHEEEDEDEED@EEEEEEEEEEEEEEEEE?;BEEE?EEEEEE?*?CA?EE:EA?'8C*:1?CEEECAAECA:CEEFFECEEEEEEEBEFFEEEEA??DDB?FFEHHFHEEHFFHDDCCC5*5+DHHFA5FA5-HHHHHGFAGHHHHHHHEHFHEEHHHHHHHFGC>FHHHHHFFFFFC5<DDDDDDB=@?????
-"""
-
-synced_barcodes = """@MISEQ03:64:000000000-A2H3D:1:1101:14358:1530 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:14206:1564 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:14943:1619 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:15764:1660 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:15201:1774 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:14225:2009 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:16656:2052 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:12555:2129 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:11781:2223 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:15819:2301 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-@MISEQ03:64:000000000-A2H3D:1:1101:19110:2311 1:N:0:TCCACAGGAGT
-TCCACAGGAGT
-+
-FFFFFFFFFFF
-"""
-
-if __name__ == '__main__':
-    main()