{"id":13703801,"url":"https://github.com/telatin/seqfu2","last_synced_at":"2025-10-21T05:19:57.375Z","repository":{"id":38180850,"uuid":"316275163","full_name":"telatin/seqfu2","owner":"telatin","description":":rocket: seqfu - Sequece Fastx Utilities","archived":false,"fork":false,"pushed_at":"2025-10-07T11:08:36.000Z","size":82014,"stargazers_count":120,"open_issues_count":0,"forks_count":9,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-10-07T11:35:52.354Z","etag":null,"topics":["bioconda","bioinformatics","bioinformatics-tool","fasta","fastq","genomics","ngs","sequencing"],"latest_commit_sha":null,"homepage":"https://telatin.github.io/seqfu2","language":"Nim","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/telatin.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2020-11-26T15:50:15.000Z","updated_at":"2025-10-07T11:08:40.000Z","dependencies_parsed_at":"2023-02-05T18:01:38.446Z","dependency_job_id":"c7edaa40-b29f-4a98-82b9-d20108645986","html_url":"https://github.com/telatin/seqfu2","commit_stats":null,"previous_names":[],"tags_count":76,"template":false,"template_full_name":null,"purl":"pkg:github/telatin/seqfu2","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/telatin%2Fseqfu2","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/telatin%2Fseqfu2/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/telatin%2Fseqfu2/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/telatin%2Fseqfu2/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/telatin","download_url":"https://codeload.github.com/telatin/seqfu2/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/telatin%2Fseqfu2/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":280207253,"owners_count":26290620,"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":"2025-10-21T02:00:06.614Z","response_time":58,"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":["bioconda","bioinformatics","bioinformatics-tool","fasta","fastq","genomics","ngs","sequencing"],"created_at":"2024-08-02T21:01:00.249Z","updated_at":"2025-10-21T05:19:57.370Z","avatar_url":"https://github.com/telatin.png","language":"Nim","readme":"\u003ca href=\"https://telatin.github.io/seqfu2\" description=\"SeqFu documentation\"\u003e\n\u003cimg align=\"right\" width=\"128\" height=\"128\" src=\"docs/img/seqfu-512.png\"\u003e\u003c/a\u003e\n\n# SeqFu\n\n[![Seqfu-Nim-Build](https://github.com/telatin/seqfu2/actions/workflows/nim-2.yaml/badge.svg)](https://github.com/telatin/seqfu2/actions/workflows/nim-2.yaml)\n![Last Commit](https://img.shields.io/github/last-commit/telatin/seqfu2)\n[![Downloads](https://img.shields.io/conda/dn/bioconda/seqfu)](https://bioconda.github.io/recipes/seqfu/README.html)\n[![Latest release](https://img.shields.io/github/v/release/telatin/seqfu2)](https://github.com/telatin/seqfu2/releases)\n\nA general-purpose program to manipulate and parse information from FASTA/FASTQ files,\nsupporting gzipped input files.\nIncludes functions to *interleave* and *de-interleave* FASTQ files, to *rename*\nsequences and to *count* and print *statistics* on sequence lengths.\n\n---\n\n## 📦 Installation\n\nSeqfu can be easily installed via Miniconda:\n\n```bash\nconda install -y -c conda-forge -c bioconda \"seqfu\u003e1.10\"\n```\n\n### Build from source\n\nBuilding the Nim programs alone would just require a `nimble build`,\nbut this would leave out some other utilities.\nThere is a `make` (Makefile) building system. Since Nim is not so popular,\nI describe a full installation:\n\n```bash\n# Do you have building tools? You will need C and make, in Ubuntu:\nsudo apt install build-essential\n\n# Install zlib\nsudo apt install zlib1g-dev\n\n# Install Nim 2.0\ncurl https://nim-lang.org/choosenim/init.sh -sSf | sh\n\n# Clone this repo\ngit clone https://github.com/telatin/seqfu2\n\n# Compile and test\ncd seqfu2\nmake\nmake test\n\n# All binaries are in bin (move them in a location in your $PATH)\n```\n\n## 📰 Citation\n\nTelatin A, Fariselli P, Birolo G.\n*SeqFu: A Suite of Utilities for the Robust\nand Reproducible Manipulation of Sequence Files*.\nBioengineering 2021, 8, 59. [doi.org/10.3390/bioengineering8050059](https://doi.org/10.3390/bioengineering8050059)\n\n```bibtex\n@article{seqfu,\n  title        = {SeqFu: A Suite of Utilities for the Robust and Reproducible Manipulation of Sequence Files},\n  author       = {Telatin, Andrea and Fariselli, Piero and Birolo, Giovanni},\n  year         = 2021,\n  journal      = {Bioengineering},\n  volume       = 8,\n  number       = 5,\n  doi          = {10.3390/bioengineering8050059},\n  issn         = {2306-5354},\n  url          = {https://www.mdpi.com/2306-5354/8/5/59},\n  article-number = 59,\n  pubmedid     = 34066939\n}\n```\n\n## 📙 Full documentation\n\n The full documentation is available at:\n[**telatin.github.io/seqfu2**](https://telatin.github.io/seqfu2)\n\n## Splash screen\n\n![`seqfu`](docs/img/screenshot-seqfu.png \"SeqFu\")\n\n","funding_links":[],"categories":["Next Generation Sequencing"],"sub_categories":["Sequence Processing"],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftelatin%2Fseqfu2","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftelatin%2Fseqfu2","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftelatin%2Fseqfu2/lists"}