{"id":17174926,"url":"https://github.com/tobiasrausch/lorax","last_synced_at":"2025-09-05T16:14:06.222Z","repository":{"id":64860292,"uuid":"450028150","full_name":"tobiasrausch/lorax","owner":"tobiasrausch","description":"A long-read analysis toolbox for cancer and population genomics","archived":false,"fork":false,"pushed_at":"2025-02-12T09:52:26.000Z","size":208,"stargazers_count":22,"open_issues_count":1,"forks_count":1,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-03-27T07:21:20.906Z","etag":null,"topics":["amplicon","bioinformatics","cancer-genomics","genomics","long-read-sequencing","long-reads","telomere"],"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":"AUTHORS","dei":null}},"created_at":"2022-01-20T09:14:36.000Z","updated_at":"2025-03-25T05:21:22.000Z","dependencies_parsed_at":"2024-03-15T16:45:52.315Z","dependency_job_id":null,"html_url":"https://github.com/tobiasrausch/lorax","commit_stats":null,"previous_names":[],"tags_count":8,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tobiasrausch%2Florax","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tobiasrausch%2Florax/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tobiasrausch%2Florax/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tobiasrausch%2Florax/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/tobiasrausch","download_url":"https://codeload.github.com/tobiasrausch/lorax/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248743655,"owners_count":21154713,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","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":["amplicon","bioinformatics","cancer-genomics","genomics","long-read-sequencing","long-reads","telomere"],"created_at":"2024-10-14T23:55:16.989Z","updated_at":"2025-04-13T16:32:32.504Z","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/lorax/README.html)\n[![Anaconda-Server Badge](https://anaconda.org/bioconda/lorax/badges/downloads.svg)](https://anaconda.org/bioconda/lorax)\n[![C/C++ CI](https://github.com/tobiasrausch/lorax/workflows/C/C++%20CI/badge.svg)](https://github.com/tobiasrausch/lorax/actions)\n[![Docker CI](https://github.com/tobiasrausch/lorax/workflows/Docker%20CI/badge.svg)](https://hub.docker.com/r/trausch/lorax/)\n[![GitHub license](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://github.com/tobiasrausch/lorax/blob/master/LICENSE)\n[![GitHub Releases](https://img.shields.io/github/release/tobiasrausch/lorax.svg)](https://github.com/tobiasrausch/lorax/releases)\n\n# Lorax: A long-read analysis toolbox for cancer and population genomics\n\nIn cancer genomics, long-read de novo assembly approaches may not be applicable because of tumor heterogeneity, normal cell contamination and aneuploid chromosomes. Generating sufficiently high coverage for each derivative, potentially sub-clonal, chromosome is not feasible. Lorax is a targeted approach to reveal complex cancer genomic structures such as telomere fusions, templated insertions or chromothripsis rearrangements. Lorax is NOT a long-read SV caller, this functionality is implemented in [delly](https://github.com/dellytools/delly).\n\n## Installing lorax\n\nLorax is available as a [statically linked binary](https://github.com/tobiasrausch/lorax/releases/), a [singularity container (SIF file)](https://github.com/tobiasrausch/lorax/releases/) or as a [docker container](https://hub.docker.com/r/trausch/lorax/). You can also build lorax from source using a recursive clone and make. Lorax depends on [HTSlib](https://github.com/samtools/htslib) and [Boost](https://www.boost.org/).\n\n`git clone --recursive https://github.com/tobiasrausch/lorax.git`\n\n`cd lorax/`\n\n`make all`\n\n## Linear reference genomes\n\nLorax has several subcommands for alignments to linear reference genomes.\n\n### Templated insertion threads\n\nTemplated insertions threads can be identified using\n\n`lorax tithreads -g hg38.fa -o tithreads.bed -m control.bam tumor.bam`\n\nThe `out.bed` file specifies nodes (templated insertion source sequences) and edges (templated insertion adjacencies) of a graph that can be plotted using dot.\n\n`cut -f 4,9 out.bed | sed -e '1s/^/graph {\\n/' | sed -e '$a}' \u003e out.dot`\n\n`dot -Tpdf out.dot -o out.pdf`\n\nThe `out.reads` file lists unique assignments of reads to templated insertion source sequences. To extract the FASTA sequences for all these reads use the `lorax extract` subcommand (below) with the `-a` option.\n\n`tail -n +2 out.reads | cut -f 1 | sort | uniq \u003e reads.lst`\n\n`lorax extract -a -g hg38.fa -r reads.lst tumor.bam`\n\n### Telomere repeats associated with complex rearrangements\n\nTelomere-associated SVs can be identified with lorax using\n\n`lorax telomere -g t2t.fa -o outprefix tumor.bam`\n\nThe output files cluster reads into distinct telomere junctions that can be locally assembled. Since telomeres are repetitive, common mis-mapping artifacts found in a panel of normal samples are provided in the `maps` subdirectory. It is recommended to use the telomere-to-telomere assembly as the reference genome for `lorax telomere`.\n\n### Read selection for targeted assembly of amplicons\n\nGiven a list of amplicon regions and a phased VCF file, lorax can be used to extract amplicon reads for targeted assembly approaches.\n\n`lorax amplicon -g hg38.fa -s sample -v phased.bcf -b amplicons.bed tumor.bam`\n\nThe amplicon subcommand outputs the selected reads (as a hash list `out.reads`) and a diagnostic table (`out.bed`) with amplicon regions and their support by split-reads. Ideally, all amplicon regions are connected and belong to one connected component (one cluster of amplicons). This amplicon graph can be plotted using dot.\n\n`cut -f 4,11 out.bed | sed -e '1s/^/graph {\\n/' | sed -e '$a}' \u003e out.dot`\n\n`dot -Tpdf out.dot -o out.pdf`\n\nTo extract the FASTA sequences for all reads use the `lorax extract` subcommand (below) with the `-a` option.\n\n### Extracting pairwise matches and FASTA sequences of reads\n\nTo get FASTA sequences and pairwise read to genome matches for a list of reads (`list.reads`) use\n\n`lorax extract -g hg38.fa -r list.reads tumor.bam`\n\nIf the read list contains hashes instead of read names as from the `lorax amplicon` subcommand then please use the `-a` command-line option.\n\n`lorax extract -a -g hg38.fa -r list.reads tumor.bam`\n\n\n## Pan-genome graphs\n\nFor pan-genome graphs and pan-genome graph alignments, lorax supports the below subcommands, some are work-in-progress.\n\n### Connected components of a pan-genome graph\n\n`lorax components pangenome.gfa.gz \u003e comp.tsv`\n\n### Converting a pan-genome (sub-)graph to dot format\n\n`lorax gfa2dot -s s103 -r 3 pangenome.gfa.gz \u003e graph.dot`\n\n`dot -Tpng graph.dot \u003e graph.png`\n\n### Converting pan-genome graph alignments to BAM\n\nWith long reads aligned to a pan-genome graph\n\n`minigraph --vc -cx lr pangenome.gfa.gz input.fastq.gz | bgzip \u003e sample.gaf.gz`\n\nlorax can be used to convert the graph alignment to BAM\n\n`lorax convert -g pangenome.gfa.gz -f input.fastq.gz sample.gaf.gz | samtools sort -o sample.bam -`\n\n### Node coverage of pan-genome graph alignments\n\n`lorax ncov -g pangenome.gfa.gz sample.gaf.gz \u003e ncov.tsv`\n\n## Citation\n\nTobias Rausch, Rene Snajder, Adrien Leger, Milena Simovic, Mădălina Giurgiu, Laura Villacorta, Anton G. Henssen, Stefan Fröhling, Oliver Stegle, Ewan Birney, Marc Jan Bonder, Aurelie Ernst, Jan O. Korbel     \nLong-read sequencing of diagnosis and post-therapy medulloblastoma reveals complex rearrangement patterns and epigenetic signatures     \nCell Genomics, 2023, 100281, [DOI: 10.1016/j.xgen.2023.100281](https://doi.org/10.1016/j.xgen.2023.100281)     \n\nLicense\n-------\nLorax is distributed under the BSD 3-Clause license. Consult the accompanying [LICENSE](https://github.com/tobiasrausch/lorax/blob/master/LICENSE) file for more details.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftobiasrausch%2Florax","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftobiasrausch%2Florax","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftobiasrausch%2Florax/lists"}