Welcome to the Hunt Lab Small RNA Pipeline Documentation

This documentation is for version 2 of the pipeline, select 1.1.0 from the version dropdown for the version 1 documentation.

This is a pipeline developed in Vicky Hunt's Lab at the University of Bath, UK to analyse small RNA data in a quick and consistent way between projects. It is deliberately designed to be highly configurable so it can be easily applied to a wide range of scenarios, though most of our work is on nematode and nematomorph worms.

Background

Most of the original methodology was devised by Mona Suleiman, Dominika Lastik and Vicky Hunt for the papers below. This was then developed into a usable pipeline by Kieran Reynolds in 2022 and updated to version 2 in 2025.

Suleiman, M., Kounosu, A., Murcott, B. et al. piRNA-like small RNAs target transposable elements in a Clade IV parasitic nematode. Sci Rep 12, 10156 (2022). https://doi.org/10.1038/s41598-022-14247-1

Lastik, D., Kounosu, A., Dayi, M. et al. Small non-coding RNAs have predicted roles in reproductive biology and transposable element regulation in the parasitic worm Strongyloides venezuelensis. Sci Rep 15, 20608 (2025). https://doi.org/10.1038/s41598-025-01968-2

Citation

This pipeline is mainly a combination of existing tools so, doesn't have a paper attached to it but can be referenced with the repository URL and version number. For example:

This analysis was performed using HuntLab-smallRNA v2.0.0 (https://github.com/Vicky-Hunt-Lab/HuntLab-smallRNA).

For the internal steps please cite the papers of the tools used:

Trim:

Martin, Marcel. (2011). CUTADAPT removes adapter sequences from high-throughput sequencing reads. EMBnet.journal. 17. 10.14806/ej.17.1.200.

Sort:

Langmead, B., Salzberg, S. Fast gapped-read alignment with Bowtie 2. Nat Methods 9, 357-359 (2012). https://doi.org/10.1038/nmeth.1923

Unitas:

Gebert, D., Hewel, C. & Rosenkranz, D. unitas: the universal tool for annotation of small RNAs. BMC Genomics 18, 644 (2017). https://doi.org/10.1186/s12864-017-4031-9

Targetid:

Langmead, B., Salzberg, S. Fast gapped-read alignment with Bowtie 2. Nat Methods 9, 357-359 (2012). https://doi.org/10.1038/nmeth.1923

Enrich:

Carlos P Cantalapiedra, Ana Hernández-Plaza, Ivica Letunic, Peer Bork, Jaime Huerta-Cepas, eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale, Molecular Biology and Evolution, Volume 38, Issue 12, December 2021, Pages 5825-5829, https://doi.org/10.1093/molbev/msab293