RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
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) 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.
iii. Download the pipeline and test it on a minimal dataset with a single command
iv. Start running your own analysis!
See usage docs for all of the available options when running the pipeline.
The nf-core/rnaseq pipeline comes with documentation about the pipeline, found in the
- Pipeline configuration
- Running the pipeline
- Output and how to interpret the results
Contributions and Support
If you would like to contribute to this pipeline, please see the contributing guidelines.
If you use nf-core/rnaseq for your analysis, please cite it using the following doi: 10.5281/zenodo.1400710
You can cite the
nf-core pre-print as follows:
Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. nf-core: Community curated bioinformatics pipelines. bioRxiv. 2019. p. 610741. doi: 10.1101/610741.