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For: Afiahayati, Sato K, Sakakibara Y. An extended genovo metagenomic assembler by incorporating paired-end information. PeerJ 2013;1:e196. [PMID: 24281688 PMCID: PMC3817583 DOI: 10.7717/peerj.196] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 10/10/2013] [Indexed: 11/25/2022]  Open
Number Cited by Other Article(s)
1
Sadurski J, Polak-Berecka M, Staniszewski A, Waśko A. Step-by-Step Metagenomics for Food Microbiome Analysis: A Detailed Review. Foods 2024;13:2216. [PMID: 39063300 PMCID: PMC11276190 DOI: 10.3390/foods13142216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 07/11/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024]  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
Kayani MUR, Huang W, Feng R, Chen L. Genome-resolved metagenomics using environmental and clinical samples. Brief Bioinform 2021;22:bbab030. [PMID: 33758906 PMCID: PMC8425419 DOI: 10.1093/bib/bbab030] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/29/2020] [Accepted: 01/20/2021] [Indexed: 12/25/2022]  Open
4
Ayling M, Clark MD, Leggett RM. New approaches for metagenome assembly with short reads. Brief Bioinform 2021;21:584-594. [PMID: 30815668 PMCID: PMC7299287 DOI: 10.1093/bib/bbz020] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 01/31/2019] [Accepted: 02/01/2019] [Indexed: 02/07/2023]  Open
5
Deng Z, Delwart E. ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data. BMC Bioinformatics 2021;22:119. [PMID: 33706720 PMCID: PMC7953547 DOI: 10.1186/s12859-021-04038-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 02/21/2021] [Indexed: 11/10/2022]  Open
6
Shah RM, McKenzie EJ, Rosin MT, Jadhav SR, Gondalia SV, Rosendale D, Beale DJ. An Integrated Multi-Disciplinary Perspectivefor Addressing Challenges of the Human Gut Microbiome. Metabolites 2020;10:E94. [PMID: 32155792 PMCID: PMC7143645 DOI: 10.3390/metabo10030094] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/18/2020] [Accepted: 02/27/2020] [Indexed: 02/06/2023]  Open
7
Cuadrat RRC, Cury JC, Dávila AMR. Metagenomic Analysis of Upwelling-Affected Brazilian Coastal Seawater Reveals Sequence Domains of Type I PKS and Modular NRPS. Int J Mol Sci 2015;16:28285-95. [PMID: 26633360 PMCID: PMC4691048 DOI: 10.3390/ijms161226101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 11/16/2015] [Accepted: 11/18/2015] [Indexed: 11/23/2022]  Open
8
Cunha MLR, Meijers JCM, Middeldorp S. Introduction to the analysis of next generation sequencing data and its application to venous thromboembolism. Thromb Haemost 2015;114:920-32. [PMID: 26446408 DOI: 10.1160/th15-05-0411] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 08/26/2015] [Indexed: 12/13/2022]
9
Lai B, Wang F, Wang X, Duan L, Zhu H. InteMAP: Integrated metagenomic assembly pipeline for NGS short reads. BMC Bioinformatics 2015;16:244. [PMID: 26250558 PMCID: PMC4545859 DOI: 10.1186/s12859-015-0686-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 07/24/2015] [Indexed: 12/03/2022]  Open
10
Afiahayati, Sato K, Sakakibara Y. MetaVelvet-SL: an extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning. DNA Res 2014;22:69-77. [PMID: 25431440 PMCID: PMC4379979 DOI: 10.1093/dnares/dsu041] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]  Open
11
Koren S, Treangen TJ, Hill CM, Pop M, Phillippy AM. Automated ensemble assembly and validation of microbial genomes. BMC Bioinformatics 2014;15:126. [PMID: 24884846 PMCID: PMC4030574 DOI: 10.1186/1471-2105-15-126] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 04/24/2014] [Indexed: 11/12/2022]  Open
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