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

Pipeline to analyze small RNAs from single-cells

A pipeline to analyse small RNA expression using Illumina sequencing data

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.

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

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

Snakemake workflow for processing small RNA-seq libaries