nf-core/smrnaseq is a bioinformatics best-practice analysis pipeline used for small RNA sequencing data.
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.
- Raw read QC (
FastQC) - Adapter trimming (
Trim Galore!)- Insert Size calculation
- Collapse reads (
seqcsluter)
- Alignment against miRBase mature miRNA (
Bowtie1) - Alignment against miRBase hairpin
- Post-alignment processing of miRBase hairpin
- Alignment against host reference genome (
Bowtie1)- Post-alignment processing of alignment against host reference genome (
SAMtools)
- Post-alignment processing of alignment against host reference genome (
- miRNA quality control (
mirtrace) - Present QC for raw read, alignment, and expression results (
MultiQC)
The nf-core/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
nf-core/smrnaseq was 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). Updated by Lorena Pantano (@lpantano) from MIT.
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.