nfcore/rnaseq repository overview

Nextflow RNA-Seq analysis pipeline, part of the nf-core community..

⁠Introduction

nf-core/rnaseq is a bioinformatics analysis pipeline used for RNA sequencing data.

The workflow processes raw data from FastQ inputs (FastQC⁠, Trim Galore!⁠), aligns the reads (STAR⁠ or HiSAT2⁠), generates counts relative to genes (featureCounts⁠, StringTie⁠) or transcripts (Salmon⁠, tximport⁠ or RSEM⁠) and performs extensive quality-control on the results (RSeQC⁠, Qualimap⁠, dupRadar⁠, Preseq⁠, edgeR⁠, MultiQC⁠). See the output documentation⁠ for more details of the results.

The pipeline is built using Nextflow⁠, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.

⁠Quick Start

i. Install nextflow⁠

ii. Install either Docker⁠ or Singularity⁠ for full pipeline reproducibility (please only use Conda⁠ as a last resort; see docs⁠)

iii. Download the pipeline and test it on a minimal dataset with a single command

nextflow run nf-core/rnaseq -profile test,<docker/singularity/conda>

iv. Start running your own analysis!

nextflow run nf-core/rnaseq -profile <docker/singularity/conda> --reads '*_R{1,2}.fastq.gz' --genome GRCh37

See usage docs⁠ for all of the available options when running the pipeline.

⁠Documentation

The nf-core/rnaseq pipeline comes with documentation about the pipeline, found in the docs/ directory:

1. Installation⁠
2. Pipeline configuration
   • Local installation⁠
   • Adding your own system config⁠
   • Reference genomes⁠
3. Running the pipeline⁠
4. Output and how to interpret the results⁠
5. Troubleshooting⁠

⁠Credits

These scripts were originally written for use at the National Genomics Infrastructure⁠, part of SciLifeLab⁠ in Stockholm, Sweden, by Phil Ewels (@ewels⁠) and Rickard Hammarén (@Hammarn⁠).

Many thanks to other who have helped out along the way too, including (but not limited to): @Galithil⁠, @pditommaso⁠, @orzechoj⁠, @apeltzer⁠, @colindaven⁠, @lpantano⁠, @olgabot⁠, @jburos⁠, @drpatelh⁠.

⁠Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines⁠.

For further information or help, don't hesitate to get in touch on Slack⁠ (you can join with this invite⁠).

⁠Citation

You can cite the nf-core publication as follows: