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Non-Coding RNA PROfiling from sRNA-seq

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ncPRO-seq is a tool for annotation and profiling of ncRNAs from smallRNA sequencing data. It aims to interrogate and perform detailed analysis on small RNAs derived from annotated non-coding regions in miRBase, piRBase, Rfam and repeatMasker, and regions defined by users. The ncPRO pipeline also has a module to identify regions significantly enriched with short reads that can not be classified as known ncRNA families.

Docker version : download and run Dockerfile (go in "Files" section)


GitHub :

ncPRO-seq Web Site


  • Support multiple Solexa, SOLiD, 454 raw reads, and Bam files
  • Reads grouping strategy (distinct vs abundant reads)
  • Quality control of raw and aligned reads
  • Reads mapping using the Bowtie software
  • More than 15 annotated organisms from mammals/metazoan to plants
  • Flexible annotation and analysis on ncRNA families from RFAM, UCSC tRNA, piRBase and miRBase
  • Annotation and analysis of repeats classes from RepeatMasker
  • Support user defined annotation files (gff3)
  • Detect regions significantly enriched with reads
  • Settings of UCSC Genome Browser tracks for visualization
  • Stand-alone/command line pipelinee and user-friendly interface
  • PDF and HTML report


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Additional Project Details

Intended Audience


Programming Language

Unix Shell, Python, Perl, AWK, S/R



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