{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,3]],"date-time":"2026-06-03T14:16:11Z","timestamp":1780496171883,"version":"3.54.1"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2016,11,7]],"date-time":"2016-11-07T00:00:00Z","timestamp":1478476800000},"content-version":"vor","delay-in-days":885,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Variant detection from next-generation sequencing (NGS) data is an increasingly vital aspect of disease diagnosis, treatment and research. Commonly used NGS-variant analysis tools generally rely on accurately mapped short reads to identify somatic variants and germ-line genotypes. Existing NGS read mappers have difficulty accurately mapping short reads containing complex variation (i.e. more than a single base change), thus making identification of such variants difficult or impossible. Insertions and deletions (indels) in particular have been an area of great difficulty. Indels are frequent and can have substantial impact on function, which makes their detection all the more imperative.<\/jats:p><jats:p>Results: We present ABRA, an assembly-based realigner, which uses an efficient and flexible localized de novo assembly followed by global realignment to more accurately remap reads. This results in enhanced performance for indel detection as well as improved accuracy in variant allele frequency estimation.<\/jats:p><jats:p>Availability and implementation: ABRA is implemented in a combination of Java and C\/C++ and is freely available for download at https:\/\/github.com\/mozack\/abra .<\/jats:p><jats:p>Contact: \u00a0lmose@unc.edu ; parkerjs@email.unc.edu<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu376","type":"journal-article","created":{"date-parts":[[2014,6,7]],"date-time":"2014-06-07T06:24:55Z","timestamp":1402122295000},"page":"2813-2815","source":"Crossref","is-referenced-by-count":149,"title":["ABRA: improved coding indel detection via assembly-based realignment"],"prefix":"10.1093","volume":"30","author":[{"given":"Lisle E.","family":"Mose","sequence":"first","affiliation":[{"name":"1 Lineberger Comprehensive Cancer Center, 2 Department of Genetics, 3 Division of Medical Oncology, Department of Internal Medicine, Multidisciplinary Thoracic Oncology Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew D.","family":"Wilkerson","sequence":"additional","affiliation":[{"name":"1 Lineberger Comprehensive Cancer Center, 2 Department of Genetics, 3 Division of Medical Oncology, Department of Internal Medicine, Multidisciplinary Thoracic Oncology Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA"},{"name":"1 Lineberger Comprehensive Cancer Center, 2 Department of Genetics, 3 Division of Medical Oncology, Department of Internal Medicine, Multidisciplinary Thoracic Oncology Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"D. Neil","family":"Hayes","sequence":"additional","affiliation":[{"name":"1 Lineberger Comprehensive Cancer Center, 2 Department of Genetics, 3 Division of Medical Oncology, Department of Internal Medicine, Multidisciplinary Thoracic Oncology Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA"},{"name":"1 Lineberger Comprehensive Cancer Center, 2 Department of Genetics, 3 Division of Medical Oncology, Department of Internal Medicine, Multidisciplinary Thoracic Oncology Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charles M.","family":"Perou","sequence":"additional","affiliation":[{"name":"1 Lineberger Comprehensive Cancer Center, 2 Department of Genetics, 3 Division of Medical Oncology, Department of Internal Medicine, Multidisciplinary Thoracic Oncology Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA"},{"name":"1 Lineberger Comprehensive Cancer Center, 2 Department of Genetics, 3 Division of Medical Oncology, Department of Internal Medicine, Multidisciplinary Thoracic Oncology Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joel S.","family":"Parker","sequence":"additional","affiliation":[{"name":"1 Lineberger Comprehensive Cancer Center, 2 Department of Genetics, 3 Division of Medical Oncology, Department of Internal Medicine, Multidisciplinary Thoracic Oncology Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA"},{"name":"1 Lineberger Comprehensive Cancer Center, 2 Department of Genetics, 3 Division of Medical Oncology, Department of Internal Medicine, Multidisciplinary Thoracic Oncology Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2014,6,6]]},"reference":[{"key":"2023041303363389200_","doi-asserted-by":"crossref","first-page":"961","DOI":"10.1101\/gr.112326.110","article-title":"Dindel: accurate indel calls from short-read data","volume":"21","author":"Albers","year":"2011","journal-title":"Genome Res."},{"key":"2023041303363389200_","doi-asserted-by":"crossref","first-page":"310","DOI":"10.1101\/gr.162883.113","article-title":"TIGRA: a targeted iterative graph routing assembler for breakpoint assembly","volume":"24","author":"Chen","year":"2014","journal-title":"Genome Res."},{"key":"2023041303363389200_","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1089\/cmb.2011.0201","article-title":"Computational techniques for human genome resequencing using mated gapped reads","volume":"19","author":"Carnevali","year":"2012","journal-title":"J. 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