nf-core pipeline · genome, references, reproducibility
nf-core/references
A bioinformatics pipeline for generating genomic indices and reference files for common organisms.
What nf-core/references is
nf-core/references is a bioinformatics pipeline designed to generate reference files and tool indices for multiple analysis workflows. It is primarily built to assemble standardised references for common organisms and store them on AWS iGenomes. The pipeline was originally written by Maxime U Garcia, Edmund Miller, and Phil Ewels.
Preparing reference assets for genomic and transcriptomic analysis often requires repeatedly running multiple indexing tools across different sequence and annotation formats. The pipeline automates the generation of aligner indices, dictionaries, interval lists, and transcript files to provide consistent reference bundles for downstream pipelines.
What the pipeline does
The pipeline processes raw reference files depending on the inputs provided. Starting from a FASTA sequence, it builds aligner indices for Bowtie1, Bowtie2, BWA-MEM, and BWA-MEM2, creates DRAGMAP hashtables, and produces FASTA index files, size metrics, GATK4 sequence dictionaries, GATK4 interval BED files, and an MSIsensor-pro list.
When a GFF3 or GTF gene annotation file is supplied alongside the FASTA sequence, the workflow converts GFF3 to GTF using GFFread, identifies splice sites with HISAT2, and generates transcript FASTA files using RSEM. It also generates indices for STAR, HISAT2, Kallisto, Salmon, and RSEM. When provided with a VCF file, the pipeline generates a corresponding Tabix index.
Key facts
- Latest release
- 0.1 (2024-12-30)
- Primary target repository
- AWS iGenomes
- FASTA indexing tools
- Bowtie1, Bowtie2, BWA-MEM, BWA-MEM2, DRAGMAP, GATK4, SAMtools, MSIsensor-pro
- Annotation indexing tools
- GFFread, HISAT2, Kallisto, RSEM, Salmon, STAR
- Variant indexing
- Tabix
What you can use it for
- DNA aligner index generation
- Building reference indices for Bowtie1, Bowtie2, BWA-MEM, BWA-MEM2, and DRAGMAP from a single FASTA file.
- Transcriptome index creation
- Producing transcript FASTAs and indices for STAR, Salmon, Kallisto, RSEM, and HISAT2 from a FASTA reference and GTF or GFF3 annotation.
- Variant calling reference setup
- Generating GATK4 dictionaries, intervals BED files, SAMtools sequence indices, and Tabix-indexed VCF files.
Run it here
The research agent runs nf-core/references 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
- Constructs a comprehensive suite of aligner and quantification indices from a unified set of input files.
- Handles both GFF3 and GTF inputs, automatically converting GFF3 files using GFFread.
- Standardises reference generation intended for community distribution through AWS iGenomes.
Watch out for
- Support for Bismark index generation is not yet implemented and remains on the development roadmap.
- Downsampling utilities for unified test dataset generation are not yet implemented.
Questions
Can I run nf-core/references without my own cluster?
The research agent runs nf-core/references 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/references under?
MIT, like every nf-core pipeline.
What inputs can be supplied to the pipeline?
The pipeline accepts a reference FASTA file, gene annotations in GTF or GFF3 format, and variant files in VCF format.
Which RNA-seq tools are supported for reference building?
The pipeline generates indices for STAR, HISAT2, Salmon, Kallisto, and RSEM, as well as extracting splice sites and transcript sequences.
Where are pipeline reference assets hosted?
Supporting assets are maintained in the references-assets repository, with the generated references primarily intended for AWS iGenomes.
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/references's own README. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.