{"id":32611504,"url":"https://github.com/ctlab/metafast","last_synced_at":"2025-10-30T13:59:26.188Z","repository":{"id":16397612,"uuid":"19148452","full_name":"ctlab/metafast","owner":"ctlab","description":"Fast metagenome analysis toolkit","archived":false,"fork":false,"pushed_at":"2023-12-12T14:44:19.000Z","size":177242,"stargazers_count":26,"open_issues_count":0,"forks_count":10,"subscribers_count":19,"default_branch":"master","last_synced_at":"2024-05-19T00:08:56.191Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Java","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/ctlab.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}},"created_at":"2014-04-25T14:15:13.000Z","updated_at":"2024-05-07T06:28:49.000Z","dependencies_parsed_at":"2023-02-14T07:15:19.959Z","dependency_job_id":"8e0d96a2-0bf8-4e21-bd0e-ee08c4398466","html_url":"https://github.com/ctlab/metafast","commit_stats":null,"previous_names":[],"tags_count":15,"template":false,"template_full_name":null,"purl":"pkg:github/ctlab/metafast","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ctlab%2Fmetafast","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ctlab%2Fmetafast/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ctlab%2Fmetafast/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ctlab%2Fmetafast/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ctlab","download_url":"https://codeload.github.com/ctlab/metafast/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ctlab%2Fmetafast/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":281818072,"owners_count":26566859,"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":"2025-10-30T02:00:06.501Z","response_time":61,"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":"2025-10-30T13:58:38.799Z","updated_at":"2025-10-30T13:59:26.177Z","avatar_url":"https://github.com/ctlab.png","language":"Java","funding_links":[],"categories":[],"sub_categories":[],"readme":"![Build](https://github.com/ctlab/metafast/actions/workflows/ant.yml/badge.svg)\n\n# MetaFast\n\n\u003cimg align=\"right\" src=\"logo.jpg\" alt=\"MetaFast\" width=\"400\"\u003e\n\n**MetaFast** (METAgenome FAST analysis toolkit) is a toolkit for calculating a number of statistics of \nmetagenome sequences and building the distance matrix between them. It also provides a functionality\nto extract features from metagenomic samples.\n\nAuthors:\n* **Software:** *Artem Ivanov*, *Sergey Kazakov* and [*Vladimir Ulyantsev*](https://ulyantsev.com), \u003cbr/\u003e\n[ITMO University](http://en.itmo.ru/en/), Saint-Petersburg, Russia.\n* **Testing:** *Veronika Dubinkina* and *Alexandr Tyakht*, \u003cbr/\u003e\nSRI of Physical-Chemical Medicine, Moscow, Russia.\n* **Idea, supervisor:** *Dmitry Alexeev*, \u003cbr/\u003e\nSRI of Physical-Chemical Medicine, Moscow, Russia.\n\n\n**MetaFast** documentation is available on the GitHub [wiki page](https://github.com/ctlab/metafast/wiki).\u003cbr/\u003e\nHere is a short version of it.\n\n\n\n## Content\n\n* [Installation](#installation)\n* [MetaFast 1.3](#metafast-13)\n* [Running instructions](#running-instructions)\n* [Examples](#examples)\n* [FAQ](#faq)\n* [Citation](#citation)\n* [Contact](#contact)\n* [License](#license)\n* [Publications using MetaFast](#publications-using-metafast)\n* [See also](#see-also)\n\n\n\n## Installation\n\nTo run MetaFast you need to have JRE 1.6 or higher installed and only one script – `metafast.sh`, `metafast.bat` or `metafast.jar`.\n\nYou can download it from the last stable release in the GitHub ['Releases' section](https://github.com/ctlab/metafast/releases).\n\n* For *Linux* and *Mac OS*: download `metafast.sh`, run the command `chmod a+x metafast.sh`, then run `./metafast.sh` from the command line.\n* For *Windows*: download `metafast.bat` and run it from the command line.\n* For other OS: download `metafast.jar` and run it via command `java -jar metafast.jar`.\n\n\nAlternatively, you can build the newest version of the MetaFast from the repository:\n~~~\ngit clone https://github.com/ctlab/metafast.git\ncd metafast\nant\n./out/metafast.sh --version\n~~~\n\n\n## MetaFast 1.3\n\nA new version of MetaFast software is being prepared for the release. New pipelines for comparative metagenomics data analysis have been implemented. Four recommended use cases (including the original one) and a detailed description of available tools are presented in [Pipelines.md](Pipelines.md)\n\n## Running instructions\n\nTo run MetaFast use the following syntax:\n* `metafast.sh [\u003cLaunch options\u003e] [\u003cInput parameters\u003e]`\n* `metafast.bat [\u003cLaunch options\u003e] [\u003cInput parameters\u003e]`\n* `java -jar metafast.jar [\u003cLaunch options\u003e] [\u003cInput parameters\u003e]`\n\nTo view help for launch options and input parameters run `metafast.sh --help` or `metafast.sh --help-all`.\n\nBy running MetaFast a working directory is created (by default `./workDir/`). \nAll intermidiate files, log file and final results are saved in it. \n\nFile `output_description.txt` is created after every run in the current and working directories. \nIt contains the description of every output file produced by the MetaFast.\n\nMetafast run script also allows you to run subtools of whole process or different tools, that was included into the package. \nTo see the list of available additional tools, run `metafast.sh --tools`.\n\n\n## Examples\n\n#### Generated _in-silico_ dataset\n\nDownload [meta_test_1.fa](https://github.com/ctlab/metafast/raw/master/test_data/meta_test_1.fa),\n[meta_test_2.fa](https://github.com/ctlab/metafast/raw/master/test_data/meta_test_2.fa) and \n[meta_test_3.fa](https://github.com/ctlab/metafast/raw/master/test_data/meta_test_3.fa) and run the command:\n~~~\n./metafast.sh -i meta_test_1.fa meta_test_2.fa meta_test_3.fa\n~~~\n\nAfter it has finished, a distance matrix can be found in `workDir/matrices/dist_matrix_\u003cdate\u003e_\u003ctime\u003e_original_order.txt`:\n~~~\n#       meta_test_1     meta_test_2     meta_test_3\nmeta_test_1     0.0000  0.5691  0.2981\nmeta_test_2     0.5691  0.0000  0.8448\nmeta_test_3     0.2981  0.8448  0.0000\n~~~\n\nThe element `matrix[i][j]` is a distance between *sample i* and *sample j*.\n\nK-mers frequency statistics is saved in `workDir/kmer-counter-many/stats/\u003cin-file\u003e.stat.txt`;\u003cbr/\u003e\nimage file with heatmap and dendrogram is saved in `workDir/matrices/dist_matrix_\u003cdate\u003e_\u003ctime\u003e_heatmap.png`:\u003cbr/\u003e\n\u003cimg src=\"test_data/meta_test_heatmap.png\" alt=\"Test heatmap\" width=\"450\"\u003e\n\n#### Mock community example\n\nFor testing on realistic metagenomic communities, the CAMI Challenge dataset was used. The detailed example description is available in file [Example.md](Example.md).\n\n## FAQ\n\n**Q** Does MetaFast works with paired-end reads?\n\n**A** Yes, MetaFast can process paired-end reads. For correct detection, files should be named with suffixes \"_R1\"\u0026\"_R2\" or \"_r1\"\u0026\"_r2\" after sample name before extension. For example, sample_r1.fastq \u0026 sample_r2.fastq, or reads_R1.fq.gz \u0026 reads_R2.fq.gz\n\n**Q** Can I compare samples with different read lengths or the number of reads?\n\n**A** Yes, you can do this without any specific preprocessing. MetaFast uses k-mers for comparing metagenomic sequences, so it will automatically normalize all values by the total number of k-mers per sample.\n\n**Q** Can I compare metagenomes obtained from different sequencing platforms (i.e. Illumina vs 454-seq)\n\n**A** Yes, you can. MetaFast extract features from each metagenome independently, so you can compare samples from different sequencing platforms.\n\n\n## Citation\n\nIf you use MetaFast in your research, please cite the following publication:\n\nUlyantsev V.I., Kazakov S.V., Dubinkina V.B., Tyakht A.V. \u0026 Alexeev D.G. (2016). \nMetaFast: fast reference-free graph-based comparison of shotgun metagenomic data. \nBioinformatics, 32(18), 2760-2767. \n[doi: 10.1093/bioinformatics/btw312](https://academic.oup.com/bioinformatics/article/32/18/2760/1743520)\n\n\n## Contact\n\nPlease report any problems directly to the GitHub [issue tracker](https://github.com/ctlab/metafast/issues). \u003cbr/\u003e\nAlso, you can send your feedback to [abivanov@itmo.ru](mailto:abivanov@itmo.ru).\n\n\n## License\n\nThe MIT License (MIT)\n\n## Publications using MetaFast\n\nThere are several papers about bioinformatics projects, which used various MetaFast pipelines for data analysis:\n\n* Analysis of human gut microbiota of patients with Crohn's disease, ulcerative colitis and healthy controls \u003cbr/\u003e\n  Khachatryan, L., Xiang, Y., Ivanov, A., Glaab, E., Graham, G., Granata, I., ... \u0026 Poussin, C. (2023). Results and lessons learned from the sbv IMPROVER metagenomics diagnostics for inflammatory bowel disease challenge. Scientific Reports, 13(1),  [doi: 10.1038/s41598-023-33050-0](https://doi.org/10.1038/s41598-023-33050-0)\n* Analysis of human gut microbiota of patients undergoing melanoma immunotherapy \u003cbr/\u003e\n  Olekhnovich, E. I., Ivanov, A. B., Babkina, A. A., Sokolov, A. A., Ulyantsev, V. I., Fedorov, D. E., \u0026 Ilina, E. N. (2023). Consistent Stool Metagenomic Biomarkers Associated with the Response To Melanoma Immunotherapy. Msystems, 8(2), e01023-22. [doi: 10.1128/msystems.01023-22](https://doi.org/10.1128/msystems.01023-22)\n* Analysis of gut microbiota time-series samples from patients undergoing microbiome transplantation\n  Olekhnovich, E. I., Ivanov, A. B., Ulyantsev, V. I., \u0026 Ilina, E. N. (2021). Separation of donor and recipient microbial diversity allows determination of taxonomic and functional features of gut microbiota restructuring following fecal transplantation. Msystems, 6(4), e00811-21. [doi: 10.1128/msystems.00811-21](https://doi.org/10.1128/msystems.00811-21)\n\n\n\n## See also\n\n* [MetaCherchant](https://github.com/ctlab/metacherchant) – a tool for analysing genomic environment within a metagenome.\n* [RECAST](https://github.com/ctlab/recast) – a tool for sorting reads per their origin in metagenomic time series.\n* [khmer](https://github.com/ged-lab/khmer) – a toolkit to split reads.\n* [crAss](http://edwards.sdsu.edu/crass/) – Cross-Assembly of Metagenomes.\n* [MaryGold](http://sourceforge.net/projects/metavar/) – Variation analysis of metagenomic samples.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fctlab%2Fmetafast","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fctlab%2Fmetafast","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fctlab%2Fmetafast/lists"}