{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,4]],"date-time":"2026-04-04T17:40:42Z","timestamp":1775324442547,"version":"3.50.1"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2022,8,17]],"date-time":"2022-08-17T00:00:00Z","timestamp":1660694400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Onur Mutlu's SAFARI Research"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,9,30]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>A genome read dataset can be quickly and efficiently remapped from one reference to another similar reference (e.g., between two reference versions or two similar species) using a variety of tools, e.g., the commonly used CrossMap tool. With the explosion of available genomic datasets and references, high-performance remapping tools will be even more important for keeping up with the computational demands of genome assembly and analysis.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We provide FastRemap, a fast and efficient tool for remapping reads between genome assemblies. FastRemap provides up to a 7.82\u00d7 speedup (6.47\u00d7, on average) and uses as low as 61.7% (80.7%, on average) of the peak memory consumption compared to the state-of-the-art remapping tool, CrossMap.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>FastRemap is written in C++. Source code and user manual are freely available at: github.com\/CMU-SAFARI\/FastRemap. Docker image available at: https:\/\/hub.docker.com\/r\/alkanlab\/fastremap. Also available in Bioconda at: https:\/\/anaconda.org\/bioconda\/fastremap-bio.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac554","type":"journal-article","created":{"date-parts":[[2022,8,17]],"date-time":"2022-08-17T13:58:50Z","timestamp":1660744730000},"page":"4633-4635","source":"Crossref","is-referenced-by-count":6,"title":["FastRemap: a tool for quickly remapping reads between genome assemblies"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6153-9008","authenticated-orcid":false,"given":"Jeremie S","family":"Kim","sequence":"first","affiliation":[{"name":"Department of Computer Engineering, ETH Zurich, D-ITET , Zurich 8006, Switzerland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6548-7863","authenticated-orcid":false,"given":"Can","family":"Firtina","sequence":"additional","affiliation":[{"name":"Department of Computer Engineering, ETH Zurich, D-ITET , Zurich 8006, Switzerland"}]},{"given":"Meryem Banu","family":"Cavlak","sequence":"additional","affiliation":[{"name":"Department of Computer Engineering, ETH Zurich, D-ITET , Zurich 8006, Switzerland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3665-6285","authenticated-orcid":false,"given":"Damla","family":"Senol Cali","sequence":"additional","affiliation":[{"name":"Department of Computer Engineering, Bionano Genomics , San Diego, CA 92121, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5443-0706","authenticated-orcid":false,"given":"Can","family":"Alkan","sequence":"additional","affiliation":[{"name":"Department of Computer Engineering, Bilkent University , Ankara 06800, Turkey"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0075-2312","authenticated-orcid":false,"given":"Onur","family":"Mutlu","sequence":"additional","affiliation":[{"name":"Department of Computer Engineering, ETH Zurich, D-ITET , Zurich 8006, Switzerland"},{"name":"Department of Computer Engineering, Bilkent University , Ankara 06800, Turkey"}]}],"member":"286","published-online":{"date-parts":[[2022,8,17]]},"reference":[{"key":"2023041408240410300_","doi-asserted-by":"crossref","first-page":"319","DOI":"10.12688\/f1000research.14148.2","article-title":"Segment_liftover: a python tool to convert segments between genome assemblies","volume":"7","author":"Gao","year":"2018","journal-title":"F1000Res"},{"key":"2023041408240410300_","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1038\/s41592-018-0046-7","article-title":"Bioconda: sustainable and comprehensive software distribution for the life sciences","volume":"15","author":"Gruning","year":"2018","journal-title":"Nat. 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