{"id":23057297,"url":"https://github.com/applicativesystem/rust-samtools-genomecapture","last_synced_at":"2025-08-15T06:32:32.213Z","repository":{"id":266343731,"uuid":"898091343","full_name":"applicativesystem/rust-samtools-genomecapture","owner":"applicativesystem","description":"rust samtools 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rust-samtools-genomecapture\n\n- rust samtools genomecapture.\n- give the id list, reference genome, upstream and downstream and extracts the reference genome portion for the genome browser. \n-  rust-samtools-genome-capture: takes a genome alignment files, a reference fasta file, the upstream and the downstream regions \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```\ncargo build \n\n```\n```\nλ gauravsablok rust-samtools-genomecapture → λ git main* → ./target/debug/rust-samtools-genome-capture -h\nUsage: rust-samtools-genome-capture \u003cALIGNMENT_ARG\u003e \u003cIDLIST_ARG\u003e \u003cFASTA_ARG\u003e \u003cUPSTREAM_ARG\u003e \u003cDOWNSTREAM_ARG\u003e \u003cREADLENGTH_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  \u003cREADLENGTH_ARG\u003e  please provide the readlength of the sequencing reads\n\nOptions:\n  -h, --help     Print help\n  -V, --version  Print version\n```\n\n\n- how to run the binary\n\n```\n./rust-samtools-genome-capture ./sample-files/Col0_C1.100k_selected.sam ./sample-files/idlist.txt ./sample-files/sample-fasta.fasta 5 10\n\n``\n- result from the rust-samtools-genome-capture\n\n```\n- selected-ids-downstream.fasta - downstream for those ids \n- selected-ids-reads.fasta - reads aligned to those ids.\n- selected-ids-upstream.fasta - upstreams for those ids.\n- selected-ids-upstream-region-downstream.fasta - upstream-region -downstream for those ids.\n\n```\nGaurav Sablok\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fapplicativesystem%2Frust-samtools-genomecapture","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fapplicativesystem%2Frust-samtools-genomecapture","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fapplicativesystem%2Frust-samtools-genomecapture/lists"}