BreakTracer: Tracing inserted sequence fragments at structural variant breakpoints using long-reads

Installing breaktracer

BreakTracer is available as a statically linked binary, as a minimal docker container or as a singularity containter (SIF file).

wget https://github.com/tobiasrausch/breaktracer/releases/download/v0.0.5/breaktracer_v0.0.5_linux_x86_64bit
chmod a+x breaktracer_v0.0.5_linux_x86_64bit
./breaktracer_v0.0.5_linux_x86_64bit

Building from source

BreakTracer can be built from source using a recursive clone and make. BreakTracer depends on HTSlib and Boost.

git clone --recursive https://github.com/tobiasrausch/breaktracer.git

cd breaktracer/

make all

Running breaktracer

BreakTracer has been designed to identify inserted sequence fragments at structural variant (SV) breakpoints using long-read sequencing data. For instance, to identify L1 fragments at SV breakpoints:

breaktracer find -n L1 -g hg38.fa input.bam > breakpoint.insertion.tsv

BreakTracer can also be used to identify a custom FASTA sequence inserted at SV breakpoints. For instance, to identify a human papillomavirus integration:

breaktracer find -e hpv.seq.fa -g hg38.fa input.bam > breakpoint.insertion.tsv

License

BreakTracer is free and open source (BSD). Consult the accompanying LICENSE file for more details.

Credits

HTSlib is heavily used for alignment processing. Boost for various data structures and algorithms and Edlib for pairwise alignments using edit distance.