https://github.com/tobiasrausch/breaktracer
Tracing inserted sequence fragments at structural variant breakpoints
https://github.com/tobiasrausch/breaktracer
flt3 insertion mobile-element-insertion mobile-elements tandem-duplication viral-genomics
Last synced: about 1 month ago
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Tracing inserted sequence fragments at structural variant breakpoints
- Host: GitHub
- URL: https://github.com/tobiasrausch/breaktracer
- Owner: tobiasrausch
- License: bsd-3-clause
- Created: 2025-07-24T08:51:58.000Z (11 months ago)
- Default Branch: main
- Last Pushed: 2026-05-05T14:23:08.000Z (about 1 month ago)
- Last Synced: 2026-05-05T15:38:28.038Z (about 1 month ago)
- Topics: flt3, insertion, mobile-element-insertion, mobile-elements, tandem-duplication, viral-genomics
- Language: C++
- Homepage:
- Size: 211 KB
- Stars: 1
- Watchers: 0
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Zenodo: .zenodo.json
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README
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# BreakTracer: Tracing inserted sequence fragments at structural variant breakpoints using long-reads
BreakTracer is designed to identify inserted sequence fragments at structural variant (SV) breakpoints using long-read sequencing data. It can detect mobile element insertions, viral sequence integrations, and internal tandem duplications (ITDs), such as FLT3-ITDs. In contrast to generic SV callers like [delly](https://github.com/dellytools/delly), BreakTracer can resolve complex SVs mediated by such insertions and link the inserted sequences to adjacent genomic rearrangements.
## Installing BreakTracer
BreakTracer is available as a [Bioconda package](https://anaconda.org/bioconda/breaktracer), as a pre-compiled [statically linked binary](https://github.com/tobiasrausch/breaktracer/releases/), as a minimal [docker container](https://hub.docker.com/r/trausch/breaktracer/) or as a [singularity containter (SIF file)](https://github.com/tobiasrausch/breaktracer/releases/). The static binaries you can simply download [here](https://github.com/tobiasrausch/breaktracer/releases/) and then make them executable, e.g.:
```
chmod a+x ./breaktracer-v0.2.8-linux-amd64
./breaktracer-v0.2.8-linux-amd64
```
## Building from source
BreakTracer can be built from source using a recursive clone and make. BreakTracer depends on [HTSlib](https://github.com/samtools/htslib) and [Boost](https://www.boost.org/).
`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 > bp.ins.vcf`
BreakTracer can also be used to identify a custom FASTA sequence inserted at SV breakpoints. For instance, to identify a human papillomavirus integration you can use
`breaktracer find -e hpv.seq.fa -g hg38.fa input.bam > bp.ins.vcf`
or with BCF output:
`breaktracer find -e hpv.seq.fa -g hg38.fa -o bp.ins.bcf input.bam`
## Other use cases
As BreakTracer also identifies plain insertions, the method can be used to detect events such as tandem duplications, for example, FLT3 internal tandem duplications (FLT3-ITDs). In this case, the duplicated FLT3 segment serves as the insertion source sequence, which can then be analyzed with BreakTracer.
```
samtools faidx hg38.fa chr13:28033983-28034368 | sed 's/>.*$/>source/' > tdsource.fa
samtools faidx tdsource.fa
```
Make sure to adjust the insertion parameters to detect small insertions (≥15bp). To speed up the analysis, you may also want to subset the BAM file to the region of interest.
```
samtools view -b input.bam chr13:28033983-28034368 > sub.bam
samtools index sub.bam
breaktracer find -m 15 -c 15 -s 15 -r 0 -e tdsource.fa -g hg38.fa sub.bam
```
## License
BreakTracer is free and open source (BSD). Consult the accompanying [LICENSE](https://github.com/tobiasrausch/breaktracer/blob/master/LICENSE) file for more details.
## Credits
[HTSlib](https://github.com/samtools/htslib) is heavily used for alignment processing. [Boost](https://www.boost.org/) for various data structures and algorithms and [Edlib](https://github.com/Martinsos/edlib) for pairwise alignments using edit distance.