{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,3,1]],"date-time":"2024-03-01T20:24:18Z","timestamp":1709324658281},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2021,5,25]],"date-time":"2021-05-25T00:00:00Z","timestamp":1621900800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01GM118568"],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01HG011392"],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,11,18]]},"abstract":"Abstract<\/jats:title>\n \n Motivation<\/jats:title>\n As more population genetics datasets and population-specific references become available, the task of translating (\u2018lifting\u2019) read alignments from one reference coordinate system to another is becoming more common. Existing tools generally require a chain file, whereas VCF files are the more common way to represent variation. Existing tools also do not make effective use of threads, creating a post-alignment bottleneck.<\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n LevioSAM is a tool for lifting SAM\/BAM alignments from one reference to another using a VCF file containing population variants. LevioSAM uses succinct data structures and scales efficiently to many threads. When run downstream of a read aligner, levioSAM is more than 7 times faster than an aligner when both are run with 16 threads.<\/jats:p>\n <\/jats:sec>\n \n Availability and implementation<\/jats:title>\n Software Package: https:\/\/github.com\/alshai\/levioSAM, Experiments: https:\/\/github.com\/langmead-lab\/levioSAM-experiments<\/jats:p>\n <\/jats:sec>\n \n Supplementary information<\/jats:title>\n Supplementary data are available at Bioinformatics online.<\/jats:p>\n <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab396","type":"journal-article","created":{"date-parts":[[2021,5,24]],"date-time":"2021-05-24T19:13:01Z","timestamp":1621883581000},"page":"4243-4245","source":"Crossref","is-referenced-by-count":6,"title":["LevioSAM: fast lift-over of variant-aware reference alignments"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"http:\/\/orcid.org\/0000-0002-3588-0883","authenticated-orcid":false,"given":"Taher","family":"Mun","sequence":"first","affiliation":[{"name":"Department of Computer Science, Johns Hopkins University , Baltimore, MD 21218, USA"}]},{"given":"Nae-Chyun","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Johns Hopkins University , Baltimore, MD 21218, USA"}]},{"ORCID":"http:\/\/orcid.org\/0000-0003-2437-1976","authenticated-orcid":false,"given":"Ben","family":"Langmead","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Johns Hopkins University , Baltimore, MD 21218, USA"}]}],"member":"286","published-online":{"date-parts":[[2021,5,25]]},"reference":[{"key":"2023051607080361600_btab396-B1","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1038\/nature15393","article-title":"A global reference for human genetic variation","volume":"526","year":"2015","journal-title":"Nature"},{"key":"2023051607080361600_btab396-B2","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/s13059-020-02229-3","article-title":"Reference flow: reducing reference bias using multiple population genomes","volume":"22","author":"Chen","year":"2021","journal-title":"Genome Biol"},{"key":"2023051607080361600_btab396-B3","doi-asserted-by":"crossref","first-page":"2156","DOI":"10.1093\/bioinformatics\/btr330","article-title":"The variant call format and vcftools","volume":"27","author":"Danecek","year":"2011","journal-title":"Bioinformatics"},{"key":"2023051607080361600_btab396-B4","doi-asserted-by":"crossref","first-page":"e1002280","DOI":"10.1371\/journal.pgen.1002280","article-title":"Phased whole-genome genetic risk in a family quartet using a major allele reference sequence","volume":"7","author":"Dewey","year":"2011","journal-title":"PLoS Genet"},{"key":"2023051607080361600_btab396-B5","doi-asserted-by":"crossref","first-page":"D876","DOI":"10.1093\/nar\/gkq963","article-title":"The UCSC genome browser database: update 2011","volume":"39","author":"Fujita","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2023051607080361600_btab396-B6","first-page":"326","author":"Gog","year":"2014"},{"key":"2023051607080361600_btab396-B7","author":"Kaminow","year":"2020"},{"key":"2023051607080361600_btab396-B8","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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