{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/commet-comparing-and-combining-multiple","title":"Commet: comparing and combining multiple metagenomic datasets","arxiv_id":"1511.08317","date":"2015-11-26","proceeding":null,"authors":[],"abstract":"Metagenomics offers a way to analyze biotopes at the genomic level and to\nreach functional and taxonomical conclusions. The bio-analyzes of large\nmetagenomic projects face critical limitations: complex metagenomes cannot be\nassembled and the taxonomical or functional annotations are much smaller than\nthe real biological diversity. This motivated the development of de novo\nmetagenomic read comparison approaches to extract information contained in\nmetagenomic datasets.\n  However, these new approaches do not scale up large metagenomic projects, or\ngenerate an important number of large intermediate and result files. We\nintroduce Commet (\"COmpare Multiple METagenomes\"), a method that provides\nsimilarity overview between all datasets of large metagenomic projects.\n  Directly from non-assembled reads, all against all comparisons are performed\nthrough an efficient indexing strategy. Then, results are stored as bit\nvectors, a compressed representation of read files, that can be used to further\ncombine read subsets by common logical operations. Finally, Commet computes a\nclusterization of metagenomic datasets, which is visualized by dendrogram and\nheatmaps.\n  Availability: http://github.com/pierrepeterlongo/commet","url_abs":"http://arxiv.org/abs/1511.08317v1","url_pdf":"http://arxiv.org/pdf/1511.08317v1.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"commet-comparing-and-combining-multiple","repo_url":"https://github.com/pierrepeterlongo/commet","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[{"task_slug":"diversity","task_name":"Diversity"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}