{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,3]],"date-time":"2024-08-03T15:07:32Z","timestamp":1722697652182},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"23","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Current sequence alignment browsers allow visualization of large and complex next-generation sequencing datasets. However, most of these tools provide inadequate display of insertions and can be cumbersome to use on large datasets. I implemented PyBamView, a lightweight Web application for visualizing short read alignments. It provides an easy-to-use Web interface for viewing alignments across multiple samples, with a focus on accurate visualization of insertions.<\/jats:p>\n               <jats:p>Availability and Implementation: PyBamView is available as a standard python package. The source code is freely available under the MIT license at https:\/\/mgymrek.github.io\/pybamview.<\/jats:p>\n               <jats:p>Contact: mgymrek@mit.edu<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu565","type":"journal-article","created":{"date-parts":[[2014,8,22]],"date-time":"2014-08-22T03:08:27Z","timestamp":1408676907000},"page":"3405-3407","source":"Crossref","is-referenced-by-count":8,"title":["PyBamView: a browser-based application for viewing short read alignments"],"prefix":"10.1093","volume":"30","author":[{"given":"Melissa","family":"Gymrek","sequence":"first","affiliation":[{"name":"1 Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, 2Harvard-MIT Division of Health Sciences and Technology, MIT, Cambridge, MA 02139 and 3Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA"},{"name":"1 Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, 2Harvard-MIT Division of Health Sciences and Technology, MIT, Cambridge, MA 02139 and 3Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA"},{"name":"1 Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, 2Harvard-MIT Division of Health Sciences and Technology, MIT, Cambridge, MA 02139 and 3Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA"}]}],"member":"286","published-online":{"date-parts":[[2014,8,21]]},"reference":[{"key":"2023012712015835100_btu565-B1","doi-asserted-by":"crossref","first-page":"819","DOI":"10.1126\/science.1231143","article-title":"Multiplex genome engineering using CRISPR\/Cas systems","volume":"339","author":"Cong","year":"2013","journal-title":"Science"},{"key":"2023012712015835100_btu565-B2","doi-asserted-by":"crossref","first-page":"865","DOI":"10.1093\/bioinformatics\/btr032","article-title":"Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM\/BAM format","volume":"27","author":"Edmonson","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012712015835100_btu565-B3","doi-asserted-by":"crossref","first-page":"2936","DOI":"10.1093\/bioinformatics\/btt515","article-title":"Consed: a graphical editor for next-generation sequencing","volume":"29","author":"Gordon","year":"2013","journal-title":"Bioinformatics"},{"key":"2023012712015835100_btu565-B4","doi-asserted-by":"crossref","first-page":"1154","DOI":"10.1101\/gr.135780.111","article-title":"lobSTR: a short tandem repeat profiler for personal genomes","volume":"22","author":"Gymrek","year":"2012","journal-title":"Genome Res."},{"key":"2023012712015835100_btu565-B5","doi-asserted-by":"crossref","first-page":"e32","DOI":"10.1093\/nar\/gks981","article-title":"Accurate human microsatellite genotypes from high-throughput resequencing data using informed error profiles","volume":"41","author":"Highnam","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023012712015835100_btu565-B6","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1101\/gr.229102","article-title":"The human genome browser at UCSC","volume":"12","author":"Kent","year":"2002","journal-title":"Genome Res."},{"key":"2023012712015835100_btu565-B7","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012712015835100_btu565-B8","doi-asserted-by":"crossref","first-page":"749","DOI":"10.1101\/gr.148718.112","article-title":"The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes","volume":"23","author":"Montgomery","year":"2013","journal-title":"Genome Res."},{"key":"2023012712015835100_btu565-B9","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1038\/nbt.1754","article-title":"Integrative genomics viewer","volume":"29","author":"Robinson","year":"2011","journal-title":"Nat. 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