Detect clusters of anomalously mapped pairs
Tabulated file format with Chromosome ID (integer from 1), name and length
Length of the first read in a pair (left read)
Length of the second read in a pair (right read)
Detection and isolation of links
Untick it if already done
Equal to at least “2µ+2√2σ
Equal to 1/2 or 1/4 of the window size
Filtering of links according different parameters and thresholds
Untick it if (the linking is) already done
for Illumina mate-pairs only
A value of 1 means all the pairs in a cluster were consistent between each other after applying filters
Converts filtered links to Circos/BED files format for graphical view of SVs

What it does

SVDetect - Version : 0.8b

Parallel version (nCPU=8)

SVDetect is a application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies

This tool aims to identifying structural variations (SVs) with both clustering and sliding-window strategies, and helping in their visualization at the genome scale. SVDetect is compatible with SOLiD and Illumina (>=1.3) reads.

Manual documentation available at the

Contact Bruno Zeitouni ( for any questions or concerns about the Galaxy implementation of SVDetect.