Small-RNA analysis

Runs with illumina small RNA-sequencing data. Aligns to the reference genome, gives QC metrics and finishes with gene count matrices.

smRNA-Seq is a bioinformatics best-practice analysis pipeline used for small RNA sequencing data analysis.
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.

When we run analysis

We run this analysis for smRNA-seq projects where we have prepared the sequencing library in-house. If you have prepared a library yourself and we are just sequencing, please get in touch and mention that you would like us to run this analysis.

The analysis works with any of the species that have a reference genome available in AWS-iGenomes. If in doubt, please ask whether we can run the pipeline for you.

Input data

bcl2fastq demultiplexed FastQ files and a genome reference.


The pipeline generates aligned BAM-files and gene count matrices, along with numerous quality control metrics. For more information, please seeĀ

Last Updated: 14th July 2023

Please read our sample submission instructions before sending samples:

Sample Submission Guidelines
Method Status


We are currently testing this method. Please contact us to find out more.

Software tool versions

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Compatible Methods