{"id":23057230,"url":"https://github.com/applicativesystem/rust-samtools-genomeview","last_synced_at":"2025-08-15T06:32:16.282Z","repository":{"id":266728738,"uuid":"898697259","full_name":"applicativesystem/rust-samtools-genomeview","owner":"applicativesystem","description":"rust-samtools-genomeview","archived":false,"fork":false,"pushed_at":"2024-12-13T21:03:27.000Z","size":15536,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2024-12-13T22:18:15.493Z","etag":null,"topics":["bioinformatics","genome-alignments","genome-analysis","genome-bioinformatics","genome-capture","genome-sequencing"],"latest_commit_sha":null,"homepage":"","language":"Rust","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/applicativesystem.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":"2024-12-04T21:34:31.000Z","updated_at":"2024-12-13T21:03:30.000Z","dependencies_parsed_at":"2024-12-05T20:30:21.106Z","dependency_job_id":null,"html_url":"https://github.com/applicativesystem/rust-samtools-genomeview","commit_stats":null,"previous_names":["applicativesystem/rust-samtools-genomeview"],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/applicativesystem%2Frust-samtools-genomeview","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/applicativesystem%2Frust-samtools-genomeview/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/applicativesystem%2Frust-samtools-genomeview/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/applicativesystem%2Frust-samtools-genomeview/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/applicativesystem","download_url":"https://codeload.github.com/applicativesystem/rust-samtools-genomeview/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":229897445,"owners_count":18141135,"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":["bioinformatics","genome-alignments","genome-analysis","genome-bioinformatics","genome-capture","genome-sequencing"],"created_at":"2024-12-16T02:11:37.374Z","updated_at":"2024-12-16T02:11:37.905Z","avatar_url":"https://github.com/applicativesystem.png","language":"Rust","funding_links":[],"categories":[],"sub_categories":[],"readme":"# rust-samtools-genomeview\n\n- rust samtools genome-view\n- rust-samtools-genome-view: takes a genome alignment files, a reference fasta file, the upstream and the downstream regions and the path to the prank aligner and then aligns the extracted regions and also outputs a unaligned file.The aligned region will also be visualized into the terminal using the embedded approach. \n- This feature is not present in samtools and specific to rust-samtools and allows for the direct estimation of the reads to alignments approach for desining capture assay.\n- targetd capture assay development for taking reads from HybSeq.\n- general note: Incase of Golang and RUST, please see the last commit message and if it says compiled binary then it is completed or else still in development version.\n\n![](https://github.com/applicativesystem/rust-samtools-genomeview/blob/main/rust-samtools-genomeview.png)\n\n```\ncargo build \n\n```\n\n```\nλ gauravsablok rust-samtools-genomeview → λ git main* → \\\n./target/debug/rust-samtools-genome-view -h\nUsage: rust-samtools-genome-view \u003cALIGNMENT_ARG\u003e \u003cIDLIST_ARG\u003e \u003cFASTA_ARG\u003e \u003cUPSTREAM_ARG\u003e \u003cDOWNSTREAM_ARG\u003e \u003cPRANK_ALIGNER_ARG\u003e\n\nArguments:\n  \u003cALIGNMENT_ARG\u003e      please provide the path to the alignment file\n  \u003cIDLIST_ARG\u003e         please provide the id list for the specific region\n  \u003cFASTA_ARG\u003e          please provide the fasta file used for the reference alignment\n  \u003cUPSTREAM_ARG\u003e       please provide the upstream add from the sam alignments to be extracted\n  \u003cDOWNSTREAM_ARG\u003e     please provide the downstream add from the sam alignments to be extracted\n  \u003cPRANK_ALIGNER_ARG\u003e  please provide the path to the prank aligner\n\nOptions:\n  -h, --help     Print help\n  -V, --version  Print version\n\n```\n\n\n- how to run the binary\n\n```\n./rust-samtools-genome-view ./sample-files/Col0_C1.100k_selected.sam ./sample-files/idlist.txt ./sample-files/sample-fasta.fasta 5 10 ./prank\n\n```\n\n- it will output following additional files\n```\n- selected-ids-downstream-aligned.fasta.best.fas - best alignment for the downstream region\n- selected-ids-reads-aligned.fasta.best.fas - best alignment for the reads\n- selected-ids-upstream-aligned.fasta.best.fas - best alignment for the upstream region.\n- selected-ids-upstream-region-downstream-aliged.fasta.best.fas - best alignment for the upstream+region+downstream.\nGaurav Sablok\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fapplicativesystem%2Frust-samtools-genomeview","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fapplicativesystem%2Frust-samtools-genomeview","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fapplicativesystem%2Frust-samtools-genomeview/lists"}