{"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/spaced-seeds-improve-k-mer-based-metagenomic","title":"Spaced seeds improve k-mer-based metagenomic classification","arxiv_id":"1502.06256","date":"2015-02-22","proceeding":null,"authors":["Karel Brinda","Maciej Sykulski","Gregory Kucherov"],"abstract":"Metagenomics is a powerful approach to study genetic content of environmental\nsamples that has been strongly promoted by NGS technologies. To cope with\nmassive data involved in modern metagenomic projects, recent tools [4, 39] rely\non the analysis of k-mers shared between the read to be classified and sampled\nreference genomes. Within this general framework, we show in this work that\nspaced seeds provide a significant improvement of classification accuracy as\nopposed to traditional contiguous k-mers. We support this thesis through a\nseries a different computational experiments, including simulations of\nlarge-scale metagenomic projects. Scripts and programs used in this study, as\nwell as supplementary material, are available from\nhttp://github.com/gregorykucherov/spaced-seeds-for-metagenomics.","url_abs":"http://arxiv.org/abs/1502.06256v3","url_pdf":"http://arxiv.org/pdf/1502.06256v3.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":"spaced-seeds-improve-k-mer-based-metagenomic","repo_url":"https://github.com/gregorykucherov/spaced-seeds-for-metagenomics","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"none","reach":null}],"tasks":[{"task_slug":"classification-1","task_name":"Classification"},{"task_slug":"classification","task_name":"General Classification"}],"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}