A pipeline for small RNA sequencing data analysis


sRNAnalyzer is a flexible, modular pipeline for the analysis of small RNA sequencing data. Features include,

  1. Additional adapter trimming process to generate cleaner data
  2. Comprehensive microRNA profiling strategies to better handle isomiR issues
  3. Summarization for each nucleotide to detect potential SNPs on miRNAs
  4. Multiple assignment to simulate miRNA array and qRT-PCR platforms
  5. A local probabilistic model to map reads to the most-likely entry IDs
  6. Comprehensive ribosomal RNA filtering to get more accurate mapping results
  7. More specific species assignment on exogenous RNAs in circulation
  8. Taxonomy annotation/summarization at major ranks for exogenous species


Download the sRNAnalyzer pipeline and alignment databases as .tar.gz files.

sRNAnalyzer PipelinesRNAnalyzer
small RNA DatabasessRNA_DBs
Human and Exogenous DatabasesMainDBs
NCBI Non-Human Databases NCBI_NonHuman
E.Coli Samples for Pipeline Evaluation E_coli_evaluation_samples

Web Application

To demonstrate how to use sRNAnalyzer, we built a web interface in a local server, which can be accessed at Web Application page for uploading data and running sRNAnalyzer pipeline online. For testing purpose, Username – ‘isb’ and Password – ‘password’ can be used. For academic use, free accounts will be provided based on email applications. Please send emails to Dr. Kai Wang.

Getting Started

To get started using sRNAnalyzer, download the sRNAnalyzer as a .zip or a .tar.gz file as well as the sRNA databases required. Then head to the Getting Started page for instruction on setting up and running sRNAnalyzer.


For more information on options and configuration, head to the Documentation. For documentation on the format of the output and summary files, go to the Output file documentation.