{"id":44983369,"url":"https://github.com/fischuu/snakebite-holoruminant-metag","last_synced_at":"2026-02-18T19:01:09.566Z","repository":{"id":260427023,"uuid":"800999952","full_name":"fischuu/Snakebite-Holoruminant-MetaG","owner":"fischuu","description":"Easy to use Snakemake metagenomic pipeline that covers a) read-based analysis b) contig based analysis and c) MAG assembly and annotation using a broad set of ready to use and included public databases and annotators","archived":false,"fork":false,"pushed_at":"2026-01-31T06:15:49.000Z","size":27793,"stargazers_count":9,"open_issues_count":20,"forks_count":1,"subscribers_count":3,"default_branch":"main","last_synced_at":"2026-01-31T20:17:52.968Z","etag":null,"topics":["dna","metagenome-assembled-genomes","metagenomics","snakemake","snakemake-workflow"],"latest_commit_sha":null,"homepage":"","language":"HTML","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/fischuu.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG","contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":"citations.tct","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2024-05-15T12:06:30.000Z","updated_at":"2026-01-31T06:15:48.000Z","dependencies_parsed_at":"2025-12-06T15:02:30.236Z","dependency_job_id":null,"html_url":"https://github.com/fischuu/Snakebite-Holoruminant-MetaG","commit_stats":null,"previous_names":["fischuu/pipeline-holoruminant-meta","fischuu/snakebite-holoruminant-metag"],"tags_count":21,"template":false,"template_full_name":null,"purl":"pkg:github/fischuu/Snakebite-Holoruminant-MetaG","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fischuu%2FSnakebite-Holoruminant-MetaG","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fischuu%2FSnakebite-Holoruminant-MetaG/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fischuu%2FSnakebite-Holoruminant-MetaG/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fischuu%2FSnakebite-Holoruminant-MetaG/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/fischuu","download_url":"https://codeload.github.com/fischuu/Snakebite-Holoruminant-MetaG/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fischuu%2FSnakebite-Holoruminant-MetaG/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29590679,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-18T18:54:29.675Z","status":"ssl_error","status_checked_at":"2026-02-18T18:50:50.517Z","response_time":162,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":["dna","metagenome-assembled-genomes","metagenomics","snakemake","snakemake-workflow"],"created_at":"2026-02-18T19:00:42.477Z","updated_at":"2026-02-18T19:01:09.558Z","avatar_url":"https://github.com/fischuu.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Overview\n\n\u003cimg src=\"resources/logo.jpeg\" alt=\"Logo\" width=\"200\" align=\"right\"/\u003e\n\nThis Snakemake pipeline dedicated to Metagenomic data analysis consists out of several modules that\ncover a) read-based b) contig-based and c) MAG-based analyses as well as quantification, quality\nchecks and a reporting module (which is currently under development). Naturally, it runs seamlessly\non HPC systems and all required software tools are bundled in docker container and/or conda\nenvironments. Further, all required databases are pre-configured and ready to be downloaded from a\ncentral place.\n\nThis makes it straight forward and as user-friendly as it can get.\n\nThe pipeline is organised in modules, which can run one-by-one. Further, the user can also choose to\nrun individual tools, giving full flexibility on how to use and run the pipeline.\n\n![Flow diagram of the pipeline](https://github.com/fischuu/Pipeline-Holoruminant-Meta/blob/main/flowchart/flowchart.png?raw=true)\n\n# Installation, Setup and running the pipeline\n\nFor a step-by-step tutorial on how to install the pipeline and all pre-compiled databases, please see\n\nGuide to install the pipeline: [Installation](https://github.com/fischuu/Pipeline-Holoruminant-Meta/blob/main/docs/02-Installation.md)\n\nGuide to prepare the configuration files: [Setup](https://github.com/fischuu/Pipeline-Holoruminant-Meta/blob/main/docs/03-Setup.md)\n\nGuide for running the pipeline: [Usage](https://github.com/fischuu/Pipeline-Holoruminant-Meta/blob/main/docs/04-Usage.md)\n\nInformation for additional tools: [Extra](https://github.com/fischuu/Pipeline-Holoruminant-Meta/blob/main/docs/05-Extra.md)\n\nFor troubleshooting, please visit the collection of most common errors: [Troubleshooting](https://github.com/fischuu/Pipeline-Holoruminant-Meta/blob/main/docs/10-Troubleshooting.md)\n\n\n# Contributions\n\nList of contributing authors:\n...\n\n\n# Contact\nPlease use the issue tracker from the GitHub or contact one of the contributors, if you'd prefer personal contact.\n\n\n## References\n\n- [`fastp`](https://github.com/OpenGene/fastp)\n- [`kraken2`](https://github.com/DerrickWood/kraken2)\n- [`SingleM`](https://github.com/wwood/singlem)\n- [`Nonpareil`](https://github.com/lmrodriguezr/nonpareil)\n- [`bowtie2`](https://github.com/BenLangmead/bowtie2)\n- [`samtools`](https://github.com/samtools/samtools)\n- [`MEGAHIT`](https://github.com/voutcn/megahit)\n- [`CONCOCT`](https://github.com/BinPro/CONCOCT)\n- [`MaxBin2`](http://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html)\n- [`MetaBat2`](https://bitbucket.org/berkeleylab/metabat)\n- [`MAGScoT`](https://github.com/ikmb/MAGScoT)\n- [`dRep`](https://github.com/MrOlm/drep)\n- [`QUAST`](https://github.com/ablab/quast)\n- [`GTDB-TK`](https://github.com/Ecogenomics/GTDBTk)\n- [`DRAM`](https://github.com/WrightonLabCSU/DRAM)\n- [`CoverM`](https://github.com/wwood/CoverM)\n- [`FastQC`](https://github.com/s-andrews/FastQC)\n- [`multiqc`](https://github.com/ewels/MultiQC)\n- [`NCyc`](https://github.com/qichao1984/NCyc)\n\n\n# Acknowledgements\nThis pipeline is a fork from the Snakemake workflow\n\nhttps://github.com/3d-omics/mg_assembly/\n\nand tailored and extended to the needs of the Holoruminant project.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffischuu%2Fsnakebite-holoruminant-metag","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ffischuu%2Fsnakebite-holoruminant-metag","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffischuu%2Fsnakebite-holoruminant-metag/lists"}