nf-core/smrnaseq is a bioinformatics best-practice analysis pipeline used for small RNA sequencing data.
The pipeline uses Nextflow, a bioinformatics workflow tool. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results.
This pipeline is primarily used with a SLURM cluster on the Swedish UPPMAX systems. However, the pipeline should be able to run on any system that Nextflow supports. We have done some limited testing using Docker and AWS, and the pipeline comes with some configuration for these systems. See the installation docs for more information.
The nfcore/smrnaseq pipeline comes with documentation about the pipeline, found in the docs/ directory:
- Installation
- Pipeline configuration
- Running the pipeline
- Output and how to interpret the results
- Troubleshooting
These scripts were originally written for use at the National Genomics Infrastructure at SciLifeLab in Stockholm, Sweden, by Phil Ewels (@ewels), Chuan Wang (@chuan-wang) and Rickard Hammarén (@Hammarn)