nf-core pipeline ·
nf-core/pacsomatic
A Nextflow pipeline for somatic variant and methylation analysis using paired PacBio HiFi tumour and normal reads.
What nf-core/pacsomatic is
nf-core/pacsomatic is a bioinformatics pipeline designed for somatic genomic analysis using Pacific Biosciences (PacBio) HiFi sequencing data. It was originally created by Wenchao Zhang and Haidong Yi within the nf-core community framework.
The pipeline addresses the requirement for integrated somatic characterisation from long-read sequencing by automatically pairing tumour and normal alignments. It enables researchers to gain insight into cancer biology through simultaneous evaluation of sequence variants, structural alterations, sample composition, and epigenetic modifications.
What the pipeline does
The workflow ingests PacBio HiFi read datasets specified through a samplesheet. Initial quality assessment is performed on raw reads using FastQC, with summary metrics aggregated and visualised through MultiQC.
Tumour and normal alignments are automatically paired to perform somatic variant calling across single-nucleotide variants (SNVs), small insertions and deletions (indels), structural variants (SVs), and copy number variations (CNVs), followed by variant annotation. Downstream steps assess tumour purity and clonality, test for homologous recombination deficiency using CHORD, and carry out methylation calling alongside differential methylation region (DMR) detection and annotation.
Key facts
- Pipeline engine
- Nextflow
- Data type
- PacBio HiFi reads
- Input format
- Samplesheet (.csv)
- Primary authors
- Wenchao Zhang and Haidong Yi
- Variant types
- SNVs, indels, SVs, and CNVs
- Epigenetic profiling
- Methylation calling and DMR detection
What you can use it for
- Somatic variant calling and annotation
- Detect and annotate somatic SNVs, indels, SVs, and CNVs from matched tumour–normal PacBio HiFi datasets.
- Homologous recombination deficiency testing
- Evaluate signs of homologous recombination deficiency in cancer genomes using the integrated CHORD tool.
- Tumour purity and clonality profiling
- Estimate the cellular purity and subclonal architecture of tumour samples relative to matched normal controls.
- Differential methylation analysis
- Call base-level DNA methylation patterns and identify differentially methylated regions between tumour and normal pairs.
Run it here
The research agent runs nf-core/pacsomatic with Nextflow on its own machine — up to 32 cores, 256 GiB of memory and 24 hours per run, which covers the test profile and real single-sample runs. It builds the samplesheet, checks it against the pipeline's schema and reads the results back. When a run is too big for one machine, it gives you the exact command for your own cluster instead.
Strengths and limits
Good at
- Combines multiple somatic alteration analyses, including SNVs, indels, SVs, and CNVs, in a unified workflow.
- Integrates genomic variation with epigenetic methylation and differential methylation region analysis.
- Automates the pairing of tumour and normal samples for downstream comparative cancer genomics.
Watch out for
- Requires paired tumour and normal data rather than standalone tumour-only datasets.
- Tailored specifically to PacBio HiFi reads rather than short-read sequencing platforms.
Questions
Can I run nf-core/pacsomatic without my own cluster?
The research agent runs nf-core/pacsomatic with Nextflow on its own machine — up to 32 cores, 256 GiB of memory and 24 hours per run, which covers the test profile and real single-sample runs. It builds the samplesheet, checks it against the pipeline's schema and reads the results back. When a run is too big for one machine, it gives you the exact command for your own cluster instead.
What licence is nf-core/pacsomatic under?
MIT, like every nf-core pipeline.
What sequencing read data does the pipeline support?
The pipeline is designed specifically to process PacBio HiFi long-read sequencing data.
Which classes of somatic mutations are detected?
It calls and annotates single-nucleotide variants, small indels, structural variations, and copy number variations.
How does the pipeline evaluate DNA methylation?
It performs methylation calling followed by differential methylation region detection and annotation across tumour and normal comparisons.
Which tools are used for initial quality control?
Read quality control is performed using FastQC, and the resulting metrics are compiled into a report using MultiQC.
How to cite it
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.
Written from nf-core/pacsomatic's own README. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.