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For: Rozov R, Goldshlager G, Halperin E, Shamir R. Faucet: streaming de novo assembly graph construction. Bioinformatics 2018;34:147-154. [PMID: 29036597 PMCID: PMC5870852 DOI: 10.1093/bioinformatics/btx471] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/21/2017] [Indexed: 11/14/2022]  Open
Number Cited by Other Article(s)
1
Song H, Tithi SS, Brown C, Aylward FO, Jensen R, Zhang L. Virseqimprover: an integrated pipeline for viral contig error correction, extension, and annotation. PeerJ 2025;13:e18515. [PMID: 39807156 PMCID: PMC11727651 DOI: 10.7717/peerj.18515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Accepted: 10/21/2024] [Indexed: 01/16/2025]  Open
2
Music of metagenomics-a review of its applications, analysis pipeline, and associated tools. Funct Integr Genomics 2021;22:3-26. [PMID: 34657989 DOI: 10.1007/s10142-021-00810-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 09/25/2021] [Accepted: 10/03/2021] [Indexed: 10/20/2022]
3
Nguyen SH, Cao MD, Coin LJM. Real-time resolution of short-read assembly graph using ONT long reads. PLoS Comput Biol 2021;17:e1008586. [PMID: 33471816 PMCID: PMC7850483 DOI: 10.1371/journal.pcbi.1008586] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 02/01/2021] [Accepted: 11/30/2020] [Indexed: 11/19/2022]  Open
4
Garimella KV, Iqbal Z, Krause MA, Campino S, Kekre M, Drury E, Kwiatkowski D, Sá JM, Wellems TE, McVean G. Detection of simple and complex de novo mutations with multiple reference sequences. Genome Res 2020;30:1154-1169. [PMID: 32817236 PMCID: PMC7462078 DOI: 10.1101/gr.255505.119] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 07/17/2020] [Indexed: 12/25/2022]
5
Wang Z, Wang Y, Fuhrman JA, Sun F, Zhu S. Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences. Brief Bioinform 2020;21:777-790. [PMID: 30860572 DOI: 10.1093/bib/bbz025] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/25/2019] [Indexed: 12/19/2022]  Open
6
Turner I, Garimella KV, Iqbal Z, McVean G. Integrating long-range connectivity information into de Bruijn graphs. Bioinformatics 2018;34:2556-2565. [PMID: 29554215 PMCID: PMC6061703 DOI: 10.1093/bioinformatics/bty157] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 11/25/2017] [Accepted: 03/14/2018] [Indexed: 12/27/2022]  Open
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