{"id":17174912,"url":"https://github.com/tobiasrausch/nrex","last_synced_at":"2025-07-10T16:36:13.437Z","repository":{"id":150205846,"uuid":"27174304","full_name":"tobiasrausch/nRex","owner":"tobiasrausch","description":"nRex: Germline and somatic single-nucleotide, short indel and structural variant calling","archived":false,"fork":false,"pushed_at":"2024-10-17T12:33:46.000Z","size":1955,"stargazers_count":12,"open_issues_count":0,"forks_count":2,"subscribers_count":3,"default_branch":"main","last_synced_at":"2024-10-31T21:35:10.447Z","etag":null,"topics":["alignment","germline","mutations","sequencing","somatic-mutations","somatic-variants","structural-variation","variant-calling"],"latest_commit_sha":null,"homepage":"","language":"Shell","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","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}},"created_at":"2014-11-26T11:42:55.000Z","updated_at":"2024-10-17T12:33:50.000Z","dependencies_parsed_at":null,"dependency_job_id":"98df7204-1678-448f-98b4-a57b144fcd68","html_url":"https://github.com/tobiasrausch/nRex","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tobiasrausch%2FnRex","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tobiasrausch%2FnRex/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tobiasrausch%2FnRex/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tobiasrausch%2FnRex/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/tobiasrausch","download_url":"https://codeload.github.com/tobiasrausch/nRex/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":223597074,"owners_count":17170872,"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":["alignment","germline","mutations","sequencing","somatic-mutations","somatic-variants","structural-variation","variant-calling"],"created_at":"2024-10-14T23:55:13.981Z","updated_at":"2024-11-07T22:03:55.886Z","avatar_url":"https://github.com/tobiasrausch.png","language":"Shell","funding_links":[],"categories":[],"sub_categories":[],"readme":"# nRex\n\nnRex is a set of script to call germline and somatic single-nucleotide variants, short indels and structural variants. The workflow is primarily for human whole-genome sequencing data (\u003e=30x) using short or long-reads.\n\n## Installing nRex\n\n`git clone --recursive https://github.com/tobiasrausch/nRex.git`\n\n`cd nRex/`\n\n`make all`\n\n## Download reference genome\n\n`cd genome/ \u0026\u0026 ./prepare_genome.sh`\n\n## Download a haplotype reference panel\n\n`cd refpanel/ \u0026\u0026 ./download.sh`\n\n`cd maps/ \u0026\u0026 ./download.sh`\n\n## Optional: VEP annotation of variants\n\nTo activate the annotation of variants using VEP, you need to download an offline annotation cache for GRCh38\n\n`make .vep`\n\n## Running nRex for GRCh38\n\nThere is a pipeline for short- and long-reads. For short-reads:\n\n`./src/nRex.sh \u003coutput prefix\u003e \u003csample1.read1.fq.gz\u003e \u003csample1.read2.fq.gz\u003e`\n\nand for long-reads:\n\n`./src/nRexLR.sh \u003coutput prefix\u003e \u003csample.fq.gz\u003e`\n\n## Postprocessing the output of the pipeline\n\nA few helper scripts to summarize the output of the various tools.\n\n### Aggregating QC statistics across multiple samples\n\n`./src/aggregate.sh table *.qc.summary`\n\n### Summarizing VEP output\n\nTo generate a table of annotated variants, you can use\n\n`python3 scripts/vep.py -v sample.vep.bcf`\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftobiasrausch%2Fnrex","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftobiasrausch%2Fnrex","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftobiasrausch%2Fnrex/lists"}