ncPRO-seq

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.

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

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GitHub : https://github.com/jbrayet/ncpro-seq

Features

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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Project Activity

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License

GNU Library or Lesser General Public License version 3.0 (LGPLv3)

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ncPRO-seq Web Site

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