nf-core pipeline ·
nf-core/radseq
A Nextflow variant-calling pipeline for restriction site-associated DNA sequencing (RADseq) data.
What nf-core/radseq is
nf-core/radseq is a bioinformatics pipeline designed to detect genetic variants from restriction site-associated DNA sequencing (RADseq) data. The pipeline is derived from dDocent, originally authored by Jon Puritz, and was implemented within the nf-core framework by Gabriel Barrett.
Restriction site-associated DNA sequencing is widely used to sample homologous genomic regions across individuals. The pipeline standardises the analysis workflow, providing containerised execution and parameterised control over quality control, reference creation, alignment, and variant identification.
What the pipeline does
Input reads first undergo quality control with FastQC, followed by adapter and quality trimming using fastp. The pipeline then accommodates two reference workflows: mapping to an existing reference genome without preprocessing, or assembling a de novo pseudoreference using CDHIT-est and Rainbow. Alignment is subsequently performed using either BWA or BWA-mem2.
Following alignment, unique molecular identifier (UMI) deduplication is carried out using UMI-tools if UMIs are present. SAMtools is used to sort, merge, and index alignment files. Target intervals are generated using BEDtools, and variant calling is executed across these regions with FreeBayes. Finally, variants are processed, sorted, and indexed using BCFtools and tabix, and overall quality metrics are collated with MultiQC.
Key facts
- Pipeline framework
- Nextflow (DSL2)
- Minimum Nextflow version
- 21.10.3
- Primary developers
- Jon Puritz (dDocent), Gabriel Barrett (nf-core/radseq)
- Input format
- Sample sheet in CSV format
- Supported aligners
- BWA, BWA-mem2
- Pseudoreference assembly tools
- CDHIT-est, Rainbow
- Variant calling software
- FreeBayes
What you can use it for
- Reference-guided RADseq analysis
- Aligning reads against an existing reference genome using BWA or BWA-mem2 to identify variants.
- De novo pseudoreference variant calling
- Constructing a de novo pseudoreference using CDHIT-est and Rainbow when an annotated reference genome is unavailable.
- UMI-tagged library processing
- Deduplicating reads derived from protocols featuring unique molecular identifiers using UMI-tools prior to calling variants.
- Sequencing quality inspection
- Evaluating raw and trimmed read qualities across multiple samples with FastQC, fastp, and MultiQC.
Run it here
The research agent runs nf-core/radseq 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
- Supports both existing reference genomes and de novo pseudoreference assembly via CDHIT-est and Rainbow.
- Provides a choice between BWA and BWA-mem2 for sequence alignment.
- Includes dedicated handling for unique molecular identifiers through UMI-tools.
- Encapsulates tasks in isolated software environments using Docker, Singularity, Podman, Shifter, Charliecloud, or Conda.
Watch out for
- Requires Nextflow version 21.10.3 or higher.
- Restricted to FreeBayes as the variant-calling engine.
Questions
Can I run nf-core/radseq without my own cluster?
The research agent runs nf-core/radseq 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/radseq under?
MIT, like every nf-core pipeline.
Does this pipeline require a reference genome?
No. The pipeline can either use an existing reference genome or generate a pseudoreference de novo from sequencing reads using CDHIT-est and Rainbow.
Which aligners can be used?
Users can select either BWA or BWA-mem2 for read alignment.
Can the pipeline process data with unique molecular identifiers?
Yes, deduplication using UMI-tools is integrated into the workflow for datasets containing UMIs.
What software calls the variants?
Variant calling is carried out using FreeBayes across intervals determined by BEDtools, with results indexed and merged using BCFtools and tabix.
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/radseq's own README. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.