{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,2]],"date-time":"2026-04-02T07:41:02Z","timestamp":1775115662003,"version":"3.50.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"21","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: When choosing a read mapper, one faces the trade off between speed and the ability to map reads in highly polymorphic regions. Here, we report NextGenMap, a fast and accurate read mapper, which reduces this dilemma. NextGenMap aligns reads reliably to a reference genome even when the sequence difference between target and reference genome is large, i.e. highly polymorphic genome. At the same time, NextGenMap outperforms current mapping methods with respect to runtime and to the number of correctly mapped reads. NextGenMap efficiently uses the available hardware by exploiting multi-core CPUs as well as graphic cards (GPUs), if available. In addition, NextGenMap handles automatically any read data independent of read length and sequencing technology.<\/jats:p>\n               <jats:p>Availability: NextGenMap source code and documentation are available at: http:\/\/cibiv.github.io\/NextGenMap\/<\/jats:p>\n               <jats:p>Contact: fritz.sedlazeck@univie.ac.at<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt468","type":"journal-article","created":{"date-parts":[[2013,8,24]],"date-time":"2013-08-24T04:09:42Z","timestamp":1377317382000},"page":"2790-2791","source":"Crossref","is-referenced-by-count":430,"title":["NextGenMap: fast and accurate read mapping in highly polymorphic genomes"],"prefix":"10.1093","volume":"29","author":[{"given":"Fritz J.","family":"Sedlazeck","sequence":"first","affiliation":[]},{"given":"Philipp","family":"Rescheneder","sequence":"additional","affiliation":[]},{"given":"Arndt","family":"von Haeseler","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2013,8,23]]},"reference":[{"key":"2023063011063501800_btt468-B1","doi-asserted-by":"crossref","first-page":"e41528","DOI":"10.1371\/journal.pone.0041528","article-title":"Advanced methylome analysis after bisulfite deep sequencing: an example in arabidopsis","volume":"7","author":"Dinh","year":"2012","journal-title":"PLoS One"},{"key":"2023063011063501800_btt468-B2","doi-asserted-by":"crossref","first-page":"3169","DOI":"10.1093\/bioinformatics\/bts605","article-title":"Tools for mapping high-throughput sequencing data","volume":"28","author":"Fonseca","year":"2012","journal-title":"Bioinformatics"},{"key":"2023063011063501800_btt468-B3","article-title":"Mason a read simulator for second generation sequencing data","author":"Holtgrewe","year":"2010","journal-title":"Technical Report TR-B-10-06, Institut f\u00fcr Mathematik und Informatik, Freie Universit\u00e4t Berlin"},{"key":"2023063011063501800_btt468-B4","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. 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