{"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/minimap2-pairwise-alignment-for-nucleotide","title":"Minimap2: pairwise alignment for nucleotide sequences","arxiv_id":"1708.01492","date":"2017-08-04","proceeding":null,"authors":["Heng Li"],"abstract":"Motivation: Recent advances in sequencing technologies promise ultra-long\nreads of $\\sim$100 kilo bases (kb) in average, full-length mRNA or cDNA reads\nin high throughput and genomic contigs over 100 mega bases (Mb) in length.\nExisting alignment programs are unable or inefficient to process such data at\nscale, which presses for the development of new alignment algorithms.\n  Results: Minimap2 is a general-purpose alignment program to map DNA or long\nmRNA sequences against a large reference database. It works with accurate short\nreads of $\\ge$100bp in length, $\\ge$1kb genomic reads at error rate $\\sim$15%,\nfull-length noisy Direct RNA or cDNA reads, and assembly contigs or closely\nrelated full chromosomes of hundreds of megabases in length. Minimap2 does\nsplit-read alignment, employs concave gap cost for long insertions and\ndeletions (INDELs) and introduces new heuristics to reduce spurious alignments.\nIt is 3-4 times faster than mainstream short-read mappers at comparable\naccuracy and $\\ge$30 times faster at higher accuracy for both genomic and mRNA\nreads, surpassing most aligners specialized in one type of alignment.\n  Availability and implementation: https://github.com/lh3/minimap2\n  Contact: hengli@broadinstitute.org","url_abs":"http://arxiv.org/abs/1708.01492v5","url_pdf":"http://arxiv.org/pdf/1708.01492v5.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":"minimap2-pairwise-alignment-for-nucleotide","repo_url":"https://github.com/lh3/minimap2","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"none","reach":{"status":"unanswered"}},{"paper_slug":"minimap2-pairwise-alignment-for-nucleotide","repo_url":"https://github.com/hasindu2008/minimap2-arm","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"none","reach":{"status":"unanswered"}},{"paper_slug":"minimap2-pairwise-alignment-for-nucleotide","repo_url":"https://github.com/stormalex/minimap2_fpga","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"none","reach":{"status":"unanswered"}}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=1708.01492","mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}