{"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/fermikit-assembly-based-variant-calling-for","title":"FermiKit: assembly-based variant calling for Illumina resequencing data","arxiv_id":"1504.06574","date":"2015-04-24","proceeding":null,"authors":[],"abstract":"Summary: FermiKit is a variant calling pipeline for Illumina data. It de novo\nassembles short reads and then maps the assembly against a reference genome to\ncall SNPs, short insertions/deletions (INDELs) and structural variations (SVs).\nFermiKit takes about one day to assemble 30-fold human whole-genome data on a\nmodern 16-core server with 85GB RAM at the peak, and calls variants in half an\nhour to an accuracy comparable to the current practice. FermiKit assembly is a\nreduced representation of raw data while retaining most of the original\ninformation.\n  Availability and implementation: https://github.com/lh3/fermikit\n  Contact: hengli@broadinstitute.org","url_abs":"http://arxiv.org/abs/1504.06574v1","url_pdf":"http://arxiv.org/pdf/1504.06574v1.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":"fermikit-assembly-based-variant-calling-for","repo_url":"https://github.com/lh3/fermikit","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}