BreakSeq2

For more information contact us at bina.rd@roche.com

Publication

            If you use BreakSeq2 in your work, please cite the following:

            Alexej Abyzov, Shantao Li, Daniel Rhee Kim, Marghoob Mohiyuddin, Adrian M. Stütz, Nicholas F. Parrish, Xinmeng Jasmine Mu, Wyatt Clark, Ken Chen, Matthew Hurles, Jan O. Korbel, Hugo Y. K. Lam, Charles Lee and Mark B. Gerstein

            Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms

            Nature CommunicationsBioinformatics published June 1, 2015 http://www.nature.com/ncomms/2015/150601/ncomms8256/full/ncomms8256.html

Download BreakSeq2

Latest version: https://github.com/bioinform/breakseq2/archive/2.2.tar.gz

For other versions, see "releases". https://github.com/bioinform/breakseq2/releases

System Requirements

The following Python packages must be installed:

pysam-0.7.7: BreakSeq2 has only been tested with version 0.7.7 of pysam.
Biopython

In addition, paths to the following tools must be provided as BreakSeq2 arguments:

BWA: Used for alignment to the breakpoint library
samtools: Used for alignment filtering. Only version 0.1.19 has been tested.

Installing BreakSeq2

BreakSeq2 is a python package and can be installed using pip. To install type pip install https://github.com/bioinform/breakseq2/archive/2.2.tar.gz. The current version of BreakSeq2 is 2.2. In general, the install source would be https://github.com/bioinform/breakseq2/archive/version.tar.gz

Running BreakSeq2

The following is the list of required options for BreakSeq2

--samtools path: Path to samtools executable.
--bwa path: Path to BWA executable.
Breakpoint library either as FASTA or GFF formats. The most up-to-date breakpoint library can be found here. When the library is in GFF format, a corresponding insertion sequence file must also be present with the suffix .ins.
--bams bam1 bam2 ...: BAMs containing read alignments.
--reference path: Reference genome in FASTA format.

Below are some examples of running BreakSeq2

Running with breakpoint library as GFF

run_breakseq2.py --reference b37.fasta --bams bwamem.bam --work work --bwa bwa-0.7.12/bwa --samtools samtools-0.1.19/samtools --bplib_gff bplib.gff --nthreads 4 --sample NA12878

Note that the sample name is not a required option. If it is missing, then the unique sample name is inferred from the BAMs. If there is no unique sample name and none is specified on the command-line, BreakSeq2 will fail. In the above example, since the breakpoint library was specified as a GFF, the insertion sequence file bplib.ins must also be present. BreakSeq2 will use the directory work for all the intermediate as well as the final output. Internally, BreakSeq2 uses the breakpoint library in FASTA format, so the conversion from GFF to FASTA is done before the actual processing. BreakSeq2 uses parallelism whenever possible for best performance-in this case, 4 threads will be used for some steps of the processing.

Running with breakpoint library as FASTA

run_breakseq2.py --reference b37.fasta --bams bwamem.bam --work work --bwa bwa-0.7.12/bwa --samtools samtools-0.1.19/samtools --bplib bplib.fa --nthreads 4

Note that since the breakpoint library was specified as a FASTA file, bplib.ins is not required here since the insertion sequences are already accounted for in the FASTA.

In general, type run_breakseq2.py -h for a list of all command-line options.