Software accompaniment to
Jin Zhang and Yufeng Wu, "SVseq: an approach for detecting exact breakpoints of deletions with low-coverage sequence data", Bioinformatics, 27(23), 3228-3234, 2011.
SVseq is a program for finding exact breakpoints of larger deletions using paired-end reads, which combines the split reads mapping and discordant insert size analysis. The first stage is split reads mapping based on the Burrows-Wheeler transform (BWT), which finds candidate deletions. The second stage filters the false positives by analyzing discordant insert sizes. See the paper for more details.
SVseq_Linux_32, executable compiled under 32 bits Linux.
SVseq_Linux_64, executable compiled under 64 bits Linux.
SVseq_Mac_OSX, executable compiled under Mac OS X.
Scripts for generating input files for SVseq
SVseq.tar.gz, a compressed file contains all the above files
Also see: SVseq2