{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T16:19:18Z","timestamp":1788279558880,"version":"build-2803163510"},"reference-count":40,"publisher":"Cold Spring Harbor Laboratory","issue":"9","funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62425107"],"award-info":[{"award-number":["62425107"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62473268"],"award-info":[{"award-number":["62473268"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["625B2039"],"award-info":[{"award-number":["625B2039"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Zhongguancun Academy","award":["20240101"],"award-info":[{"award-number":["20240101"]}]},{"name":"Zhongguancun Academy","award":["20240310"],"award-info":[{"award-number":["20240310"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genome Res."],"accepted":{"date-parts":[[2026,7,21]]},"published-print":{"date-parts":[[2026,9]]},"abstract":"<jats:p>\n                    Partial order alignment (POA) has emerged as a fundamental component in long-read error correction, assembly and pangenomics. However, conventional POA algorithms are limited by high time and memory requirements, making them inefficient for large-scale data sets. Here, we present minipoa, a fast and memory-efficient POA tool that incorporates seed-chain-align heuristics, adaptive or static banding strategies, and single-instruction multiple-data optimizations. Minipoa achieves up to a fivefold speedup over abPOA, reduces memory usage by up to 16-fold, and improves correction accuracy, while maintaining strong performance on both Pacific Biosciences and Oxford Nanopore Technologies simulated data sets, and can be readily integrated into existing long-read error correction and assembly workflows. In multiple sequence alignment data sets, minipoa demonstrates highly competitive computational efficiency and alignment accuracy, achieving total column scores up to 2.5-fold higher compared with MAFFT in low-similarity scenarios. Moreover, minipoa enables multiple sequence alignment of megabase-long genomes and million-sequence data sets, demonstrated by 342\n                    <jats:italic>Mycobacterium tuberculosis<\/jats:italic>\n                    sequences and 1 million SARS-CoV-2 sequences, respectively. Collectively, minipoa is well positioned to become a cornerstone in the era of large-scale pangenomics.\n                  <\/jats:p>","DOI":"10.1101\/gr.282046.126","type":"journal-article","created":{"date-parts":[[2026,7,24]],"date-time":"2026-07-24T14:55:20Z","timestamp":1784904920000},"page":"1849-1862","source":"Crossref","is-referenced-by-count":0,"title":["Fast and memory efficient partial order alignment with minipoa"],"prefix":"10.1101","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0009-0003-9233-5288","authenticated-orcid":false,"given":"Haodong","family":"Liu","sequence":"first","affiliation":[{"name":"Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China;"},{"name":"Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324000, Zhejiang, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-1788-3084","authenticated-orcid":false,"given":"Pinglu","family":"Zhang","sequence":"additional","affiliation":[{"name":"Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China;"},{"name":"Zhongguancun Academy, Beijing 100094, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4843-3350","authenticated-orcid":false,"given":"Yanming","family":"Wei","sequence":"additional","affiliation":[{"name":"Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324000, Zhejiang, China;"},{"name":"School of Computer Science and Technology, Xidian University, Xi'an, Shaanxi 710126, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-8073-3582","authenticated-orcid":false,"given":"Qinzhong","family":"Tian","sequence":"additional","affiliation":[{"name":"Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China;"},{"name":"Zhongguancun Academy, Beijing 100094, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5068-5672","authenticated-orcid":false,"given":"Yixiao","family":"Zhai","sequence":"additional","affiliation":[{"name":"School of Mechanical Engineering, Tongji University, Shanghai 200092, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6406-1142","authenticated-orcid":false,"given":"Quan","family":"Zou","sequence":"additional","affiliation":[{"name":"Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China;"},{"name":"Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324000, Zhejiang, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9175-4649","authenticated-orcid":false,"given":"Mengting","family":"Niu","sequence":"additional","affiliation":[{"name":"Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China;"},{"name":"Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324000, Zhejiang, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"246","published-online":{"date-parts":[[2026,7,24]]},"reference":[{"key":"2026090108351219000_36.9.1849.1","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-5193(89)80196-1"},{"key":"2026090108351219000_36.9.1849.2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-08148-z"},{"key":"2026090108351219000_36.9.1849.3","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-025-64547-z"},{"key":"2026090108351219000_36.9.1849.4","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.2474"},{"key":"2026090108351219000_36.9.1849.5","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbae473"},{"key":"2026090108351219000_36.9.1849.6","doi-asserted-by":"publisher","DOI":"10.1145\/322358.322360"},{"key":"2026090108351219000_36.9.1849.7","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkl244"},{"key":"2026090108351219000_36.9.1849.8","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkh340"},{"key":"2026090108351219000_36.9.1849.9","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msp098"},{"key":"2026090108351219000_36.9.1849.10","unstructured":"Foley BT , Korber BTM , Leitner TK , Apetrei C , Hahn B , Mizrachi I , Mullins J , Rambaut A , Wolinsky S . 2018. 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