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Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.
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This pipeline has moved!

This pipeline has been moved to the new nf-core project. You can now find it here:

If you have any problems with the pipeline, please create an issue at the above repository instead.

To find out more about nf-core, visit

This repository will be archived to maintain the released versions for future reruns, in the spirit of full reproducibility.

If you have any questions, please get in touch:

// Phil Ewels, 2018-08-20


NGI-RNAseq is a bioinformatics analysis pipeline used for RNA sequencing data.

It pre-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 pipeline was written at the National Genomics Infastructure at SciLifeLab Stockholm, Sweden.


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

  1. Installation
  2. Pipeline configuration
  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 developed by Phil Ewels (@ewels) and Rickard Hammarén (@Hammarn). Docker and AWS integration was led by Denis Moreno (@Galithil) and Phil Ewels (@ewels).

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

Participating Institutes

NGI-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
Quantitative Biology Center (QBiC), Germany

SciLifeLab National Genomics Infrastructure