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For: Wala J, Beroukhim R. SeqLib: a C ++ API for rapid BAM manipulation, sequence alignment and sequence assembly. Bioinformatics 2017;33:751-753. [PMID: 28011768 DOI: 10.1093/bioinformatics/btw741] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 11/18/2016] [Indexed: 11/14/2022]  Open
Number Cited by Other Article(s)
1
Liu Y, Shen X, Gong Y, Liu Y, Song B, Zeng X. Sequence Alignment/Map format: a comprehensive review of approaches and applications. Brief Bioinform 2023;24:bbad320. [PMID: 37668049 DOI: 10.1093/bib/bbad320] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/16/2023] [Accepted: 08/18/2023] [Indexed: 09/06/2023]  Open
2
Pitman A, Huang X, Marth GT, Qiao Y. quickBAM: a parallelized BAM file access API for high-throughput sequence analysis informatics. Bioinformatics 2023;39:btad463. [PMID: 37498562 PMCID: PMC10412403 DOI: 10.1093/bioinformatics/btad463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/31/2023] [Accepted: 07/26/2023] [Indexed: 07/28/2023]  Open
3
Sibbesen JA, Eizenga JM, Novak AM, Sirén J, Chang X, Garrison E, Paten B. Haplotype-aware pantranscriptome analyses using spliced pangenome graphs. Nat Methods 2023;20:239-247. [PMID: 36646895 DOI: 10.1101/2021.03.26.437240] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 11/28/2022] [Indexed: 05/24/2023]
4
Linderman MD, Paudyal C, Shakeel M, Kelley W, Bashir A, Gelb BD. NPSV: A simulation-driven approach to genotyping structural variants in whole-genome sequencing data. Gigascience 2021;10:giab046. [PMID: 34195837 PMCID: PMC8246072 DOI: 10.1093/gigascience/giab046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 05/04/2021] [Accepted: 06/07/2021] [Indexed: 12/20/2022]  Open
5
Dewhurst SM, Yao X, Rosiene J, Tian H, Behr J, Bosco N, Takai KK, de Lange T, Imieliński M. Structural variant evolution after telomere crisis. Nat Commun 2021;12:2093. [PMID: 33828097 PMCID: PMC8027843 DOI: 10.1038/s41467-021-21933-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 02/17/2021] [Indexed: 01/14/2023]  Open
6
Wala JA, Bandopadhayay P, Greenwald NF, O'Rourke R, Sharpe T, Stewart C, Schumacher S, Li Y, Weischenfeldt J, Yao X, Nusbaum C, Campbell P, Getz G, Meyerson M, Zhang CZ, Imielinski M, Beroukhim R. SvABA: genome-wide detection of structural variants and indels by local assembly. Genome Res 2018. [PMID: 29535149 PMCID: PMC5880247 DOI: 10.1101/gr.221028.117] [Citation(s) in RCA: 274] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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