nfcore/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 gene counts (featureCounts, StringTie) and performs extensive quality-control on the results (RSeQC, dupRadar, Preseq, edgeR, MultiQC). See the output documentation for more details of the results.

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

The nfcore/RNAseq pipeline comes with documentation about the pipeline, found in the docs/ directory:

1. Installation
2. Pipeline configuration
   • Local installation
   • Amazon Web Services (aws)
   • Swedish UPPMAX clusters
   • Swedish cs3e Hebbe cluster
   • Tübingen QBiC
   • Adding your own system
3. Running the pipeline
4. Output and how to interpret the results
5. Troubleshooting

These scripts were written at the National Genomics Infrastructure, part of SciLifeLab in Stockholm, Sweden. The pipeline was initially developed 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.

nfcore/RNAseq is now used by a number of core sequencing and bioinformatics facilities. Some of these are listed below. If you use this pipeline too, please let us know in an issue and we will add you to the list.

	National Genomics Infrastructure (NGI), Sweden	https://ngisweden.scilifelab.se/
	Quantitative Biology Center (QBiC), Germany	https://portal.qbic.uni-tuebingen.de/portal/