{"id":16285167,"url":"https://github.com/kdm9/seqhax","last_synced_at":"2025-09-02T01:33:04.821Z","repository":{"id":20381118,"uuid":"23656724","full_name":"kdm9/seqhax","owner":"kdm9","description":"Small sequence analysis tools that don't deserve their own repos.","archived":false,"fork":false,"pushed_at":"2024-04-23T08:39:59.000Z","size":2423,"stargazers_count":8,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-07-03T03:03:09.243Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"C","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/kdm9.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":"2014-09-04T09:40:17.000Z","updated_at":"2024-04-23T08:40:02.000Z","dependencies_parsed_at":"2024-10-10T19:22:42.443Z","dependency_job_id":"208fd898-6e92-41e8-8fac-881c96795fed","html_url":"https://github.com/kdm9/seqhax","commit_stats":null,"previous_names":[],"tags_count":39,"template":false,"template_full_name":null,"purl":"pkg:github/kdm9/seqhax","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kdm9%2Fseqhax","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kdm9%2Fseqhax/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kdm9%2Fseqhax/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kdm9%2Fseqhax/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/kdm9","download_url":"https://codeload.github.com/kdm9/seqhax/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kdm9%2Fseqhax/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273218428,"owners_count":25065913,"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","status":"online","status_checked_at":"2025-09-01T02:00:09.058Z","response_time":120,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":[],"created_at":"2024-10-10T19:22:32.637Z","updated_at":"2025-09-02T01:33:04.783Z","avatar_url":"https://github.com/kdm9.png","language":"C","funding_links":[],"categories":[],"sub_categories":[],"readme":"Seqhax\n======\n\nA seqtk-style toolkit for sequence analysis. By no means feature complete. In\nfact largely contains features other authors have not implemented in their\nrespective tools.\n\nInstallation\n============\n\nSeqhax is packaged in bioconda, please `mamba install -c bioconda seqhax` if conda is working for you. Otherwise, static binaries are uploaded by the CI to github releases. Or, you can build it yourself:\n\n```bash\nsudo apt-get install zlib1g-dev libhts-dev libhtscodecs-dev  # Or whatever equivalent for your system\ngit clone https://github.com/kdmurray91/seqhax.git\ncd seqhax\nmkdir build \u0026\u0026 cd build\ncmake ..\nmake\nmake install\n```\n\nTo make static binaries, one can use `cmake -DSTATIC_BUILD=On ..` in the above series of commands.\n\nAny other issues, file a [bug report on github](https://github.com/kdmurray91/seqhax/issues).\n\nDocumentation\n=============\n\nThere are two commands in this package: `seqhax` and `htshax`. \n\n## `seqhax`\n\nThe `seqhax` command contains various sequence file manipulation subcommands. The commands, along with a synopsis\nof their actions, are displayed when one types `seqhax` with no arguments. \nAt the time of writing, these were:\n\n```\n$ seqhax\nUSAGE:\n    seqhax PROGRAM [options]\n\nwhere PROGRAM is one of:\n    anon       -- Rename sequences by a sequential number\n    convert    -- Convert between FASTA and FASTQ formats\n    clihist    -- Records a histogram of stdin.\n    filter     -- Filter reads from a sequence file\n    pairs      -- (De)interleave paired end reads\n    pecheck    -- Check that paired end reads match properly\n    preapp     -- Prepend or append string to sequences\n    randseq    -- Generate a random sequence file\n    rebarcode  -- Add index sequences from header to the start of reads\n    stats      -- Basic statistics about sequence files\n    trunc      -- Truncate sequences\n```\n\nThe usage of each subcommand can be obtained using the `-h` flag to that\nsubcommand, e.g. `seqhax preapp -h`. \n\nSome brief description of the more involved commands is below.\n\n#### `pairs`\n\nInterleaves or de-interleaves paired reads. Converts between the following\nforms:\n\n- Separate R1/R2 paired files and single read read file.\n- \"Strict\" interleaved file, where failed/missing reads are replaced with a\n  single 'N'.\n- \"Broken paired\" interleaved files, where failed/missing reads are simply not\n  present.\n\n#### `pecheck`\n\nChecks that read pairs are correctly matched, between split (R1 \u0026 R2) files, or\ninterleaved files. Optionally, can be used to join multiple R1/R2 from the\nsample sample into a single interleaved file, while checking read IDs match.\n\n## `htshax`\n\n`htshax` consists of various utilities for the handling of HTS formats via HTSlib. These are mostly things that I wish samtools/bcftools would do, but don't.\n\n```\n$ htshax\nUsage\n    htshax PROGRAM [options]\n\nwhere PROGRAM is one of:\n\nbcfhist -- Calculate histograms on MAF allele freq and missingness across samples\n```\n\n#### `bcfhist`\n\nCreate histograms over various V/BCF metrics used in variant filtering (`QUAL`, `ALLELE_FREQ`, `F_MISSING`, `INFO/DP`). Nominally bcftools stats could do this, but it doesn't summarise missingness, so I wrote this quick tool to do so.\n\n# License\n\nGPL v3 (see ./LICENSE).\n\nCopyright (c) 2014-2023 Kevin Murray.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkdm9%2Fseqhax","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkdm9%2Fseqhax","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkdm9%2Fseqhax/lists"}