{"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/metapalette-a-k-mer-painting-approach-for","title":"MetaPalette: A $k$-mer painting approach for metagenomic taxonomic profiling and quantification of novel strain variation","arxiv_id":"1602.05328","date":"2016-02-17","proceeding":null,"authors":[],"abstract":"Metagenomic profiling is challenging in part because of the highly uneven\nsampling of the tree of life by genome sequencing projects and the limitations\nimposed by performing phylogenetic inference at fixed taxonomic ranks. We\npresent the algorithm MetaPalette which uses long $k$-mer sizes ($k=30, 50$) to\nfit a $k$-mer \"palette\" of a given sample to the $k$-mer palette of reference\norganisms. By modeling the $k$-mer palettes of unknown organisms, the method\nalso gives an indication of the presence, abundance, and evolutionary\nrelatedness of novel organisms present in the sample. The method returns a\ntraditional, fixed-rank taxonomic profile which is shown on independently\nsimulated data to be one of the most accurate to date. Tree figures are also\nreturned that quantify the relatedness of novel organisms to reference\nsequences and the accuracy of such figures is demonstrated on simulated\nspike-ins and a metagenomic soil sample. The software implementing MetaPalette\nis available at: https://github.com/dkoslicki/MetaPalette. Pre-trained\ndatabases are included for Archaea, Bacteria, Eukaryota, and viruses.","url_abs":"http://arxiv.org/abs/1602.05328v1","url_pdf":"http://arxiv.org/pdf/1602.05328v1.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":"metapalette-a-k-mer-painting-approach-for","repo_url":"https://github.com/dkoslicki/MetaPalette","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[],"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}