{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,9]],"date-time":"2025-11-09T03:22:13Z","timestamp":1762658533951,"version":"3.37.3"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2021,10,3]],"date-time":"2021-10-03T00:00:00Z","timestamp":1633219200000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004189","name":"Max Planck Society","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004189","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,11,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Bisulfite sequencing data provide value beyond the straightforward methylation assessment by analyzing single-read patterns. Over the past years, various metrics have been established to explore this layer of information. However, limited compatibility with alignment tools, reference genomes or the measurements they provide present a bottleneck for most groups to routinely perform read-level analysis. To address this, we developed RLM, a fast and scalable tool for the computation of several frequently used read-level methylation statistics. RLM supports standard alignment tools, works independently of the reference genome and handles most sequencing experiment designs. RLM can process large input files with a billion reads in just a few hours on common workstations.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/github.com\/sarahet\/RLM.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab663","type":"journal-article","created":{"date-parts":[[2021,9,30]],"date-time":"2021-09-30T20:54:33Z","timestamp":1633035273000},"page":"3934-3935","source":"Crossref","is-referenced-by-count":6,"title":["RLM: fast and simplified extraction of read-level methylation metrics from bisulfite sequencing data"],"prefix":"10.1093","volume":"37","author":[{"given":"Sara","family":"Hetzel","sequence":"first","affiliation":[{"name":"Department of Genome Regulation, Max Planck Institute for Molecular Genetics , Berlin, Germany"}]},{"given":"Pay","family":"Giesselmann","sequence":"additional","affiliation":[{"name":"Department of Genome Regulation, Max Planck Institute for Molecular Genetics , Berlin, Germany"}]},{"given":"Knut","family":"Reinert","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Informatics, Freie Universit\u00e4t , Berlin, Germany"}]},{"given":"Alexander","family":"Meissner","sequence":"additional","affiliation":[{"name":"Department of Genome Regulation, Max Planck Institute for Molecular Genetics , Berlin, Germany"},{"name":"Department of Biology, Chemistry and Pharmacy, Freie Universit\u00e4t , Berlin, Germany"},{"name":"Department of Stem Cell and Regenerative Biology, Harvard University , Cambridge, MA 02138, USA"},{"name":"Broad Institute of MIT and Harvard , Cambridge, MA 02142, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0723-4980","authenticated-orcid":false,"given":"Helene","family":"Kretzmer","sequence":"additional","affiliation":[{"name":"Department of Genome Regulation, Max Planck Institute for Molecular Genetics , Berlin, Germany"}]}],"member":"286","published-online":{"date-parts":[[2021,10,2]]},"reference":[{"key":"2023051607344520700_btab663-B1","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1038\/s41594-018-0046-4","article-title":"Global delay in nascent strand DNA methylation","volume":"25","author":"Charlton","year":"2018","journal-title":"Nat. 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