{"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/fast-and-accurate-alignment-of-long-bisulfite","title":"Fast and accurate alignment of long bisulfite-seq reads","arxiv_id":"1401.1129","date":"2014-01-06","proceeding":null,"authors":["Brent S. Pedersen","Kenneth Eyring","Subhajyoti De","Ivana V. Yang","David A. Schwartz"],"abstract":"Summary: Longer sequencing reads, with at least 200 bases per template are\nnow common. While traditional aligners have adopted new strategies to improve\nthe mapping of longer reads, aligners specific to bisulfite-sequencing were\noptimized when much shorter reads were the norm. We sought to perform the first\ncomparison using longer reads to determine which aligners were most accurate\nand efficient and to evaluate a novel software tool, bwa-meth, built on a\ntraditional mapper that supports insertions, deletions and clipped alignments.\nWe gauge accuracy by comparing the number of on and off-target reads from a\ntargeted sequencing project and by simulations. Availability and\nImplementation: The benchmarking scripts and the bwa-meth software are\navailable at https://github/com/brentp/bwa-meth/ under the MIT License.","url_abs":"http://arxiv.org/abs/1401.1129v2","url_pdf":"http://arxiv.org/pdf/1401.1129v2.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":"fast-and-accurate-alignment-of-long-bisulfite","repo_url":"https://github.com/brentp/bwa-meth","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"none","reach":null},{"paper_slug":"fast-and-accurate-alignment-of-long-bisulfite","repo_url":"https://github.com/FAANG/GSM-pipeline","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"none","reach":null},{"paper_slug":"fast-and-accurate-alignment-of-long-bisulfite","repo_url":"https://github.com/FAANG/proj-gs-meth","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"none","reach":null},{"paper_slug":"fast-and-accurate-alignment-of-long-bisulfite","repo_url":"https://github.com/nf-core/methylseq","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"none","reach":null},{"paper_slug":"fast-and-accurate-alignment-of-long-bisulfite","repo_url":"https://github.com/zhongmicai/Methylation_notes","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"none","reach":null}],"tasks":[{"task_slug":"benchmarking","task_name":"Benchmarking"}],"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}