nf-core pipeline · archived · exome, exome-sequencing, genomics
nf-core/exoseq
A Nextflow bioinformatics pipeline for exome sequencing analysis and variant calling following GATK best practices.
What nf-core/exoseq is
nf-core/exoseq is a bioinformatics analysis pipeline designed for processing exome sequencing data. Built using the Nextflow workflow manager, it implements standard Genome Analysis Toolkit (GATK) best-practice workflows for germline or somatic genetic variant identification.
The pipeline was initially developed by Senthilkumar Panneerselvam at the National Genomics Infrastructure within SciLifeLab in Stockholm, with contributions from Phil Ewels. It was subsequently extended by Alex Peltzer and Marie Gauder at QBiC Tübingen, as well as Marc Höppner at IKMB Kiel.
The repository has been archived and is no longer maintained. Users and contributors are directed towards the nf-core/sarek pipeline for current exome and genomics analysis needs.
What the pipeline does
The pipeline processes exome sequencing reads through several sequential steps based on GATK best practices. It begins with sequence alignment, followed by duplicate marking, base quality score recalibration, and local realignment.
After read pre-processing, the pipeline conducts variant calling, followed by variant filtration, variant evaluation, and variant annotation.
Key facts
- Status
- Archived — no longer maintained
- Workflow manager
- Nextflow
- Core methodology
- GATK best practices
- Primary application
- Exome sequencing variant calling
- Initial developer
- Senthilkumar Panneerselvam (SciLifeLab)
- Key contributors
- Phil Ewels, Alex Peltzer, Marie Gauder, Marc Höppner
What you can use it for
- Exome sequence alignment and pre-processing
- Aligns raw sequencing reads, marks duplicate fragments, and performs base quality recalibration alongside local realignment.
- GATK-based variant calling
- Identifies genetic variants from aligned exome sequencing datasets following established GATK best-practice workflows.
- Variant filtering and evaluation
- Filters identified variants and evaluates call sets to generate annotated variant summaries.
Strengths and limits
Good at
- Standardises exome sequence processing according to GATK best-practice guidelines.
- Implemented in Nextflow to provide reproducible pipeline execution across different compute environments.
- Accommodates custom exome capture kits during pipeline execution.
Watch out for
- The pipeline is archived and no longer maintained.
- Users are advised to use or contribute to nf-core/sarek instead of this workflow.
Questions
Can I run nf-core/exoseq without my own cluster?
The research agent runs nf-core/exoseq 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/exoseq under?
MIT, like every nf-core pipeline.
Is nf-core/exoseq actively developed?
No, the repository is archived and is no longer maintained.
What replacement pipeline should be used instead?
Researchers are advised to consider using or contributing to nf-core/sarek for exome analysis.
What core steps are performed during execution?
The pipeline runs sequence alignment, duplicate marking, recalibration, realignment, variant calling, filtration, evaluation, and variant annotation.
Can custom exome capture kits be used?
Yes, documentation exists within the project for preparing and using custom exome capture kits.
Written from nf-core/exoseq's own README. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.