ewels/ngi-rnaseq repository overview

⁠Introduction

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.

⁠Documentation

The NGI-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

⁠Credits

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.

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