A small-RNA sequencing analysis pipeline

Small non-coding RNA annotation Pipeline Optimized for rRNA- and tRNA-Derived Small RNAs

A comprehensive collection of long inverted repeats in 424 eukaryotic genomes

A toolset for handling sequencing data with unique molecular identifiers (UMIs)

JBrowse plugin that supports smallRNA alignments

A pipeline to analyse small RNA expression using Illumina sequencing data

Pipeline to analyze small RNAs from single-cells

R Markdown files for analyses of rice small RNA, gene expression and DNA methylation

Analysis of small RNA-seq in C. elegans

CBS-miRSeq: a robust comprehensive bioinformatics pipeline for microRNA expression profiling by next generation sequencing.

The scramAligner pipeline is designer to align small RNA reads to references sequences with no mis-matches. There is no requirement for reference index building. The pipeline is ideally suited to analysis of siRNAs generated from transgenes or viruses. Scripts for visualising alignments are also provided

A little script that looks for piRNA clusters based on small RNA library coverage

Snakemake workflow for processing small RNA-seq libaries