{"id":30593407,"url":"https://github.com/tobiasrausch/breaktracer","last_synced_at":"2026-05-05T16:01:42.923Z","repository":{"id":306226140,"uuid":"1025437041","full_name":"tobiasrausch/breaktracer","owner":"tobiasrausch","description":"Tracing inserted sequence fragments at structural variant breakpoints","archived":false,"fork":false,"pushed_at":"2026-05-05T14:23:08.000Z","size":216,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"main","last_synced_at":"2026-05-05T15:38:28.038Z","etag":null,"topics":["flt3","insertion","mobile-element-insertion","mobile-elements","tandem-duplication","viral-genomics"],"latest_commit_sha":null,"homepage":"","language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/tobiasrausch.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":".zenodo.json","notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2025-07-24T08:51:58.000Z","updated_at":"2026-05-05T14:01:19.000Z","dependencies_parsed_at":"2025-07-24T13:16:59.755Z","dependency_job_id":"24fc819c-442a-4302-a547-f1bf1d09e36f","html_url":"https://github.com/tobiasrausch/breaktracer","commit_stats":null,"previous_names":["tobiasrausch/breaktracer"],"tags_count":11,"template":false,"template_full_name":null,"purl":"pkg:github/tobiasrausch/breaktracer","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tobiasrausch%2Fbreaktracer","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tobiasrausch%2Fbreaktracer/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tobiasrausch%2Fbreaktracer/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tobiasrausch%2Fbreaktracer/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/tobiasrausch","download_url":"https://codeload.github.com/tobiasrausch/breaktracer/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tobiasrausch%2Fbreaktracer/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":32656654,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-05T11:29:49.557Z","status":"ssl_error","status_checked_at":"2026-05-05T11:29:48.587Z","response_time":54,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["flt3","insertion","mobile-element-insertion","mobile-elements","tandem-duplication","viral-genomics"],"created_at":"2025-08-29T18:13:57.867Z","updated_at":"2026-05-05T16:01:42.917Z","avatar_url":"https://github.com/tobiasrausch.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square)](http://bioconda.github.io/recipes/breaktracer/README.html)\n[![Anaconda-Server Badge](https://anaconda.org/bioconda/breaktracer/badges/downloads.svg)](https://anaconda.org/bioconda/breaktracer)\n[![C/C++ CI](https://github.com/tobiasrausch/breaktracer/workflows/C/C++%20CI/badge.svg)](https://github.com/tobiasrausch/breaktracer/actions)\n[![Docker CI](https://github.com/tobiasrausch/breaktracer/workflows/Docker%20CI/badge.svg)](https://hub.docker.com/r/trausch/breaktracer/)\n[![GitHub license](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://github.com/tobiasrausch/breaktracer/blob/master/LICENSE)\n[![GitHub Releases](https://img.shields.io/github/release/tobiasrausch/breaktracer.svg)](https://github.com/tobiasrausch/breaktracer/releases)\n\n# BreakTracer: Tracing inserted sequence fragments at structural variant breakpoints using long-reads\n\nBreakTracer 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.\n\n## Installing BreakTracer\n\nBreakTracer 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.:\n\n```\nchmod a+x ./breaktracer-v0.2.8-linux-amd64\n./breaktracer-v0.2.8-linux-amd64\n```\n\n## Building from source\n\nBreakTracer 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/).\n\n`git clone --recursive https://github.com/tobiasrausch/breaktracer.git`\n\n`cd breaktracer/`\n\n`make all`\n\n## Running BreakTracer\n\nBreakTracer 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:\n\n`breaktracer find -n L1 -g hg38.fa input.bam \u003e bp.ins.vcf`\n\nBreakTracer 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\n\n`breaktracer find -e hpv.seq.fa -g hg38.fa input.bam \u003e bp.ins.vcf`\n\nor with BCF output:\n\n`breaktracer find -e hpv.seq.fa -g hg38.fa -o bp.ins.bcf input.bam`\n\n## Other use cases\n\nAs 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.\n\n```\nsamtools faidx hg38.fa chr13:28033983-28034368 | sed 's/\u003e.*$/\u003esource/' \u003e tdsource.fa\nsamtools faidx tdsource.fa\n```\n\nMake 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.\n\n```\nsamtools view -b input.bam chr13:28033983-28034368 \u003e sub.bam\nsamtools index sub.bam\nbreaktracer find -m 15 -c 15 -s 15 -r 0 -e tdsource.fa -g hg38.fa sub.bam\n```\n\n## License\n\nBreakTracer is free and open source (BSD). Consult the accompanying [LICENSE](https://github.com/tobiasrausch/breaktracer/blob/master/LICENSE) file for more details.\n\n\n## Credits\n\n[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.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftobiasrausch%2Fbreaktracer","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftobiasrausch%2Fbreaktracer","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftobiasrausch%2Fbreaktracer/lists"}