{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,6]],"date-time":"2026-06-06T11:13:35Z","timestamp":1780744415859,"version":"3.54.1"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2019,8,9]],"date-time":"2019-08-09T00:00:00Z","timestamp":1565308800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["R21AI117407"],"award-info":[{"award-number":["R21AI117407"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["NS105781"],"award-info":[{"award-number":["NS105781"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["1F31NS108797"],"award-info":[{"award-number":["1F31NS108797"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>While next-generation sequencing (NGS) has dramatically increased the availability of genomic data, phased genome assembly and structural variant (SV) analyses are limited by NGS read lengths. Long-read sequencing from Pacific Biosciences and NGS barcoding from 10x Genomics hold the potential for far more comprehensive views of individual genomes. Here, we present MsPAC, a tool that combines both technologies to partition reads, assemble haplotypes (via existing software) and convert assemblies into high-quality, phased SV predictions. MsPAC represents a framework for haplotype-resolved SV calls that moves one step closer to fully resolved, diploid genomes.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/github.com\/oscarlr\/MsPAC.<\/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\/btz618","type":"journal-article","created":{"date-parts":[[2019,8,8]],"date-time":"2019-08-08T11:35:30Z","timestamp":1565264130000},"page":"922-924","source":"Crossref","is-referenced-by-count":23,"title":["MsPAC: a tool for haplotype-phased structural variant detection"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4587-6124","authenticated-orcid":false,"given":"Oscar L","family":"Rodriguez","sequence":"first","affiliation":[{"name":"Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai , New York, NY 10029, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna","family":"Ritz","sequence":"additional","affiliation":[{"name":"Biology Department, Reed College , Portland, OR 97202, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew J","family":"Sharp","sequence":"additional","affiliation":[{"name":"Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai , New York, NY 10029, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ali","family":"Bashir","sequence":"additional","affiliation":[{"name":"Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai , New York, NY 10029, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,8,9]]},"reference":[{"key":"2023013110091891200_btz618-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":"2023013110091891200_btz618-B2","doi-asserted-by":"crossref","first-page":"34.","DOI":"10.1186\/2047-217X-3-34","article-title":"Rapid detection of structural variation in a human genome using nanochannel-based genome mapping technology","volume":"3","author":"Cao","year":"2014","journal-title":"GigaScience"},{"key":"2023013110091891200_btz618-B3","doi-asserted-by":"crossref","first-page":"238.","DOI":"10.1186\/1471-2105-13-238","article-title":"Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory","volume":"13","author":"Chaisson","year":"2012","journal-title":"BMC Bioinform"},{"key":"2023013110091891200_btz618-B4","doi-asserted-by":"crossref","first-page":"608","DOI":"10.1038\/nature13907","article-title":"Resolving the complexity of the human genome using single-molecule sequencing","volume":"517","author":"Chaisson","year":"2015","journal-title":"Nature"},{"key":"2023013110091891200_btz618-B5","doi-asserted-by":"crossref","first-page":"1784.","DOI":"10.1038\/s41467-018-08148-z","article-title":"Multi-platform discovery of haplotype-resolved structural variation in human genomes","volume":"10","author":"Chaisson","year":"2019","journal-title":"Nat. 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