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.
- Align reads to reference with minimap2
- Assemble (trio-binned) haploid genomes with hifiasm (HiFi only)
- Call SNVs & joint genotyping with deepvariant and GLNexus
- Call SVs with Severus or Sniffles2
- Call CNVs with HiFiCNV
- Call tandem repeats with TRGT (HiFi only)
- Call paralogous genes with Paraphase
- Call variants from assembly with dipcall (HiFi only)
- Annotate SNVs and INDELs with databases of choice, i.e. gnomAD, CADD etc. with echtvar and VEP
- Annotate repeat expansions with stranger
- Annotate SVs with SVDB and VEP
- Rank SNVs, INDELs and SVs with GENMOD
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
NIST,HG002,/path/to/HG002.fastq.gz,FAM1,HG003,HG004,1,2
NIST,HG005,/path/to/HG005.bam,FAM1,HG003,HG004,2,1
Supply a reference genome with --fasta and choose a matching --preset for your data (revio, pacbio, ONT_R10). 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> \
--fasta <reference.fasta> \
--outdir <OUTDIR>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:
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 it using the following doi: 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 docs/CITATIONS.md file.