{"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/ngs-based-haplotype-assembly-using-matrix","title":"NGS Based Haplotype Assembly Using Matrix Completion","arxiv_id":"1801.09864","date":"2018-01-30","proceeding":null,"authors":["Sina Majidian","MH Kahaei"],"abstract":"We use matrix completion methods for haplotype assembly from NGS reads to\ndevelop the new HapSVT, HapNuc, and HapOPT algorithms. This is performed by\napplying a mathematical model to convert the reads to an incomplete matrix and\nestimating unknown components. This is followed by quantizing and decoding the\ncompleted matrix in order to generate haplotypes. These algorithms are compared\nto the recently addressed SDhaP algorithm for the real fosmid data. It is shown\nthat reconstruction rate and the MSE of these algorithms outperform the SDhaP.\nAlso, the MEC score of the HapOPT is lower than that of the SDhaP with almost\nthe same running time.","url_abs":"http://arxiv.org/abs/1801.09864v1","url_pdf":"http://arxiv.org/pdf/1801.09864v1.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":"ngs-based-haplotype-assembly-using-matrix","repo_url":"https://github.com/smajidian/HapMC","is_official":1,"mentioned_in_paper":0,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[{"task_slug":"matrix-completion","task_name":"Matrix Completion"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}