nanoporcini/conf/params.yml at master · aringeri/nanoporcini · GitHub

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qualityFiltering:
  ITS1:
    minQualityPhred: 20
    minLength: 90
    maxLength: 2000
  ITS2:
    minQualityPhred: 20
    minLength: 90
    maxLength: 2000
  FULL_ITS:
    minQualityPhred: 20
    minLength: 300
    maxLength: 6000
  LSU:
    minQualityPhred: 20
    minLength: 900
qc_quality_profile: false
qc_plot_sample_level: false
sample_barcode_in_file_name: false
primers:
#  fwd: "CTTGGTCATTTAGAGGAAGTAA" # ITSF1 (5'->3')
#  rev_rc: "CCCGTCTTGAAACACGG" # LRU3 (reverse complement)
  fwd: "AACTTAAAGGAATTGACGGAAG" # NS5 (SSU)
  rev_rc: "GGTAAGCAGAACTGGCG" # LRU6 (reverse complement)
region:
  LSU:
    classifier: "dada2"
    rdp_trained_model_dir: "$baseDir/data/db/RDP-LSU/RDPClassifier_fungiLSU_trainsetNo11_trained/"
chimera_filtering:
  ref_db: "${baseDir}/data/db/unite2024/unite2024ITS.fasta"
subsample:
  enabled: true
  type: uneven
  scenarios:
    - count: 100
      seed: 93
      mixin:
        '20221208.Rep1_Run2_ITS_Fungal_database.Trichomonascus_ciferrii.BC77':
          prop: 0.05
        '20221208.Rep1_Run2_ITS_Fungal_database.Erysiphe_necator.BC35':
          prop: 0.1
        '20221208.Rep1_Run2_ITS_Fungal_database.Eutypa_lata.BC39':
          prop: 0.2
        '20221208.Rep1_Run2_ITS_Fungal_database.Penicillium_chrysogenum.BC71':
          prop: 0.5
        '20221208.Rep1_Run2_ITS_Fungal_database.Candid_zeylanoides.BC57':
          prop: 1
    - count: 200
      seed: 8745
      mixin:
        '20221208.Rep1_Run2_ITS_Fungal_database.Trichomonascus_ciferrii.BC77':
          prop: 0.025
        '20221208.Rep1_Run2_ITS_Fungal_database.Erysiphe_necator.BC35':
          prop: 0.05
        '20221208.Rep1_Run2_ITS_Fungal_database.Eutypa_lata.BC39':
          prop: 0.1
        '20221208.Rep1_Run2_ITS_Fungal_database.Penicillium_chrysogenum.BC71':
          prop: 0.25
        '20221208.Rep1_Run2_ITS_Fungal_database.Candid_zeylanoides.BC57':
          prop: 0.5
    - count: 500
      seed: 77
      mixin:
        '20221208.Rep1_Run2_ITS_Fungal_database.Trichomonascus_ciferrii.BC77':
          prop: 0.01
        '20221208.Rep1_Run2_ITS_Fungal_database.Erysiphe_necator.BC35':
          prop: 0.02
        '20221208.Rep1_Run2_ITS_Fungal_database.Eutypa_lata.BC39':
          prop: 0.04
        '20221208.Rep1_Run2_ITS_Fungal_database.Penicillium_chrysogenum.BC71':
          prop: 0.1
        '20221208.Rep1_Run2_ITS_Fungal_database.Candid_zeylanoides.BC57':
          prop: 0.2
    - count: 1000
      seed: 42
      mixin:
        '20221208.Rep1_Run2_ITS_Fungal_database.Trichomonascus_ciferrii.BC77':
          prop: 0.005
        '20221208.Rep1_Run2_ITS_Fungal_database.Erysiphe_necator.BC35':
          prop: 0.01
        '20221208.Rep1_Run2_ITS_Fungal_database.Eutypa_lata.BC39':
          prop: 0.02
        '20221208.Rep1_Run2_ITS_Fungal_database.Penicillium_chrysogenum.BC71':
          prop: 0.05
        '20221208.Rep1_Run2_ITS_Fungal_database.Candid_zeylanoides.BC57':
          prop: 0.1
    - count: 2000
      seed: 4
      # 5, 10, 20, 50, 100
      mixin:
        '20221208.Rep1_Run2_ITS_Fungal_database.Trichomonascus_ciferrii.BC77':
          prop: 0.0025
        '20221208.Rep1_Run2_ITS_Fungal_database.Erysiphe_necator.BC35':
          prop: 0.005
        '20221208.Rep1_Run2_ITS_Fungal_database.Eutypa_lata.BC39':
          prop: 0.01
        '20221208.Rep1_Run2_ITS_Fungal_database.Penicillium_chrysogenum.BC71':
          prop: 0.025
        '20221208.Rep1_Run2_ITS_Fungal_database.Candid_zeylanoides.BC57':
          prop: 0.05
  repetitions: 1
cluster:
  methods:
    - vsearch
    - nanoclust
  hdbscan:
    min_cluster_sizes: [5, 10, 20, 50, 100]
  vsearch:
    min_cluster_size: 1
  gather_min_cluster_size_stats: false
  shuffle:
    enabled: false
    seed: 14
consensus:
  num_polishing_reads: 200
  methods: []
taxonomic_assignment:
  enabled: false
  dnabarcoder:
    ref_db: 'data/db/unite2024/unite2024ITS.fasta'
    ref_classifications: 'data/db/unite2024/unite2024ITS.classification'
    cutoffs: 'data/db/dnabarcoder/unite2024ITS.unique.cutoffs.best.json'
extract:
  ITS1: false
  ITS2: false
  FULL_ITS: true
  LSU: false
exclude:
  - '20221208.Rep1_Run2_ITS_Fungal_database.Aspergillus_niger.BC44'
  - '20221208.Rep1_Run2_ITS_Fungal_database.Cryptococcus_albidus.BC58'
  - '20221208.Rep1_Run2_ITS_Fungal_database.Galactomyces_geotrichum.BC64'
  - '20221208.Rep1_Run2_ITS_Fungal_database.Meyerozyma_guillermondii.BC69'
  - '20221208.Rep1_Run2_ITS_Fungal_database.Yarrowia_lipolytica.BC82'
  - '20221208.Rep1_Run2_ITS_Fungal_database.Fusarium_proliferatum.BC63'
  - '20221208.Rep1_Run2_ITS_Fungal_database.Puccinia_triticina.BC26'
# replicate species
  - '20221208.Rep1_Run2_ITS_Fungal_database.Austropuccinia_psidii.BC36'
  - '20221208.Rep1_Run2_ITS_Fungal_database.Cryptococcus_gattii_VG_III.BC60'
  - '20221208.Rep1_Run2_ITS_Fungal_database.Cryptococcus_neoformans_VNI.BC61'