analysis, annotation, visualization of small RNA sequencing experiments

discover and chararacterize small RNAs from sequencing

SPAR: pipeline for small RNA-seq, short total RNA-seq, miRNA-seq, single-cell small RNA-seq data processing, analysis, annotation, visualization, and comparison against reference ENCODE and DASHR datasets.
SPAR Webserver: Interactive analyses and visualization of small RNA sequencing data

Fast turn-around analyses for small RNA-seq, microRNA-seq, single-cell small RNA, short total RNA sequencing data, and comparison of the user-given sequencing data to reference data from DASHR normal human tissues/cell types and human ENCODE cell lines.

Getting started

To get started, select and analyze a reference small RNA-seq dataset from ENCODE and DASHR or analyze your own small RNA dataset by uploading or providing a URL for web-accessible small RNA data. See tutorials for examples on how to use SPAR and prepare your data for analysis.


  • August 23, 2018: DASHR v2.0 database has been released. SPAR has been used to process all small RNA sequencing experiments integrated into DASHR v2.0 (>800 libraries across 185 tissues and cell types for both GRCh37/hg19 and GRCh38/hg38 genome assemblies).
  • June 15, 2018: PNGC blog post about SPAR
  • June 06, 2018: SPAR is now available on OmicsTools SPAR on OmicsTools
  • May 07, 2018: News article about SPAR web server in RNA-Seq Blog news Read here SPAR RNA-seq blog article
  • April 16, 2018: SPAR manuscript has been accepted for publication in NAR Web Server issue (2018) SPAR manuscript
  • April 06, 2018: SPAR pipeline code and scripts are now available at SPAR repository
  • April 02, 2018: Tutorials for preparing small RNA data for SPAR analysis have been added
  • Jan 31, 2018: Tutorials have been added with examples on how to use SPAR for various analysis cases
  • Dec 20, 2017: SPAR 1.0 released. Release notes


If you use SPAR in your research or publications, please cite:

Pavel P. Kuksa, Alexandre Amlie-Wolf, Zivadin Katanic, Otto Valladares, Li-San Wang, Yuk Yee Leung. SPAR: small RNA-seq portal for analysis of sequencing experiments. NAR 2018 (Web Server issue).