Introduction

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.

Pipeline summary

  1. Raw read QC (FastQC)
  2. Adapter trimming (Trim Galore!)
  3. Alignment against miRBase mature miRNA (Bowtie1)
    1. Post-alignment processing of miRBase mature miRNA counts (SAMtools)
    2. Analysis on miRBase mature miRNA counts (edgeR)
      • TMM normalization and a table of top expression mature miRNA
      • MDS plot clustering samples
      • Heatmap of sample similarities
  4. Alignment against miRBase hairpin for the unaligned reads in step 3 (Bowtie1)
    1. Post-alignment processing of miRBase hairpin counts (SAMtools)
    2. Analysis on miRBase hairpin counts (edgeR)
      • TMM normalization and a table of top expression hairpin
      • MDS plot clustering samples
      • Heatmap of sample similarities
  5. Alignment against host reference genome (Bowtie1)
    1. Post-alignment processing of alignment against host reference genome (SAMtools)
  6. Visualization of alignment statistics (NGI-Visualization)
  7. miRNA quality control (mirtrace)
  8. Present QC for raw read, alignment, and expression results (MultiQC)

Documentation

The nf-core/smrnaseq 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

Credits

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).

It is been updated by Lorena Pantano (@lpantano).