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Mapping such reads onto a reference genome is one of the most fundamental tasks in sequence analysis. Mapping sensitivity is becoming a major concern since high sensitivity can detect more aligned regions on the reference and obtain more aligned bases, which are useful for downstream analysis. In this study, we present pathMap, a novel k-mer graph-based mapper that is specifically designed for mapping SMS reads with high sensitivity. By viewing the alignment chain as a path containing as many anchors as possible in the matched k-mer graph, pathMap treats chaining as a path selection problem in the directed graph. pathMap iteratively searches the longest path in the remaining nodes; more candidate chains with high quality can be effectively detected and aligned. Compared to other state-of-the-art mapping methods such as minimap2 and Winnowmap2, experiment results on simulated and real-life datasets demonstrate that pathMap obtains the number of mapped chains at least 11.50% more than its closest competitor and increases the mapping sensitivity by 17.28% and 13.84% of bases over the next-best mapper for Pacific Biosciences and Oxford Nanopore sequencing data, respectively. In addition, pathMap is more robust to sequence errors and more sensitive to species- and strain-specific identification of pathogens using MinION reads.<\/jats:p>","DOI":"10.1093\/bib\/bbae107","type":"journal-article","created":{"date-parts":[[2024,3,22]],"date-time":"2024-03-22T14:56:47Z","timestamp":1711119407000},"source":"Crossref","is-referenced-by-count":0,"title":["pathMap: a path-based mapping tool for long noisy reads with high sensitivity"],"prefix":"10.1093","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0261-0529","authenticated-orcid":false,"given":"Ze-Gang","family":"Wei","sequence":"first","affiliation":[{"name":"School of Physics and Opto-Electronics Technology, Baoji University of Arts and Sciences , Baoji, 721016 , China"},{"name":"Division of Biomedical Engineering , Department of Computer Science and Department of Mechanical Engineering, , Saskatoon, SK S7N 5A9 , Canada"},{"name":"University of Saskatchewan , Department of Computer Science and Department of Mechanical Engineering, , Saskatoon, SK S7N 5A9 , Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiao-Dan","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Physics and Opto-Electronics Technology, Baoji University of Arts and Sciences , Baoji, 721016 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xing-Guo","family":"Fan","sequence":"additional","affiliation":[{"name":"School of Physics and Opto-Electronics Technology, Baoji University of Arts and Sciences , Baoji, 721016 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yu","family":"Qian","sequence":"additional","affiliation":[{"name":"School of Physics and Opto-Electronics Technology, Baoji University of Arts and Sciences , Baoji, 721016 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fei","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Physics and Opto-Electronics 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