genomic-medicine-sweden/nallo is a bioinformatics analysis pipeline for long-reads from both PacBio and (targeted) ONT-data, focused on rare-disease. Heavily influenced by best-practice pipelines such as nf-core/sarek, nf-core/raredisease, nf-core/nanoseq, PacBio Human WGS Workflow, epi2me-labs/wf-human-variation and brentp/rare-disease-wf.
- Call SNVs & joint genotyping with deepvariant and GLNexus
- Call SVs with Severus, Sniffles or Sawfish (PacBio only)
- Call CNVs with HiFiCNV
- Call tandem repeats with TRGT (PacBio only) or STRdust
- Call paralogous genes with Paraphase (PacBio only)
- Phase and haplotag reads with LongPhase, whatshap or HiPhase
- Create methylation pileups with modkit or pbcpgtools (PacBio only)
- Rare methylation analaysis with methbat profile (PacBio only)
- Annotate SNVs and INDELs with databases of choice, e.g. gnomAD, ClinVar, CADD with echtvar and VEP
- Annotate repeat expansions with strdrop and stranger (TRGT only)
- Annotate SVs with SVDB and VEP
- Rank SNVs, INDELs, SVs and CNVs with GENMOD
- Filter SNVs, INDELs, SVs and CNVs with filter_vep and bcftools
Note
If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.
Prepare a samplesheet with input data:
samplesheet.csv
project,sample,file,family_id,paternal_id,maternal_id,sex,phenotype
my_project,HG002,/path/to/HG002.fastq.gz,NIST,HG003,HG004,1,2
my_project,HG003,/path/to/HG003.bam,NIST,0,0,1,1
my_project,HG004,/path/to/HG004.bam,NIST,0,0,2,1
Supply a reference genome with --fasta and choose a matching --preset for your data (revio, pacbio, ONT_R10 or ONT_R10_AS). Now, you can run the pipeline using:
nextflow run genomic-medicine-sweden/nallo \
-profile <docker/singularity/.../institute> \
--input samplesheet.csv \
--preset <revio/pacbio/ONT_R10/ONT_R10_AS> \
--fasta <reference.fasta> \
--outdir <OUTDIR>However, to run most parts of the pipeline you will need to supply additional reference files. For more details and further functionality, please refer to the documentation.
genomic-medicine-sweden/nallo was originally written by Felix Lenner.
We thank the following people for their extensive assistance in the development of this pipeline: Anders Jemt, Annick Renevey, Daniel Schmitz, Lucía Peña-Pérez, Peter Pruisscher, Ramprasad Neethiraj, Alexander Koc & Sofia Demmou.
If you would like to contribute to this pipeline, please see the contributing guidelines.
If you use genomic-medicine-sweden/nallo for your analysis, please cite:
Nallo: a Nextflow pipeline for comprehensive human long-read genome analysis
Felix Lenner, Anders Jemt, Lucia Peña Pérez, Ramprasad Neethiraj, Peter Pruisscher, Daniel Schmitz, Annick Renevey, Pádraic Corcoran, Daniel Nilsson, Jesper Eisfeldt, Anna Lindstrand, Valtteri Wirta, Adam Ameur, Lars Feuk.
Bioinformatics, Volume 42, Issue 3, March 2026, btag086, https://doi.org/10.1093/bioinformatics/btag086
Specific versions of the pipeline can be referenced via zenodo: 10.5281/zenodo.13748210.
This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.
The nf-core framework for community-curated bioinformatics pipelines.
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.
An extensive list of references for the tools used by the pipeline can be found in the Software Versions section of the MultiQC report generated with the pipeline.