breakdancer | SV detection from paired end | Genomics library

breakdancer is a C++ library typically used in Artificial Intelligence, Genomics applications. breakdancer has no bugs, it has no vulnerabilities and it has low support. You can download it from GitHub.

Usage: breakdancer_max Options: -o STRING operate on a single chromosome [all chromosome] -s INT minimum length of a region [7] -c INT cutoff in unit of standard deviation [3] -m INT maximum SV size [1000000000] -q INT minimum alternative mapping quality [35] -r INT minimum number of read pairs required to establish a connection [2] -x INT maximum threshold of haploid sequence coverage for regions to be ignored [1000] -b INT buffer size for building connection [100] -t only detect transchromosomal rearrangement, by default off -d STRING prefix of fastq files that SV supporting reads will be saved by library -g STRING dump SVs and supporting reads in BED format for GBrowse -l analyze Illumina long insert (mate-pair) library -a print out copy number by bam file rather than library, by default on -h print out Allele Frequency column, by default off -y INT output score filter [40].