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For: Pandey P, Bender MA, Johnson R, Patro R. deBGR: an efficient and near-exact representation of the weighted de Bruijn graph. Bioinformatics 2017;33:i133-i141. [PMID: 28881995 PMCID: PMC5870571 DOI: 10.1093/bioinformatics/btx261] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]  Open
Number Cited by Other Article(s)
1
Xie P, Guo Y, Teng Y, Zhou W, Yu Y. GeneMiner: A tool for extracting phylogenetic markers from next-generation sequencing data. Mol Ecol Resour 2024;24:e13924. [PMID: 38197287 DOI: 10.1111/1755-0998.13924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 12/14/2023] [Accepted: 12/21/2023] [Indexed: 01/11/2024]
2
Pibiri GE. On weighted k-mer dictionaries. Algorithms Mol Biol 2023;18:3. [PMID: 37328897 DOI: 10.1186/s13015-023-00226-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/13/2023] [Indexed: 06/18/2023]  Open
3
Lu Y, Ge C, Cai B, Xu Q, Kong R, Chang S. Antibody sequences assembly method based on weighted de Bruijn graph. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023;20:6174-6190. [PMID: 37161102 DOI: 10.3934/mbe.2023266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
4
Zhang Z, Xie P, Guo Y, Zhou W, Liu E, Yu Y. Easy353: A Tool to Get Angiosperms353 Genes for Phylogenomic Research. Mol Biol Evol 2022;39:6862883. [PMID: 36458838 PMCID: PMC9757696 DOI: 10.1093/molbev/msac261] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/28/2022] [Accepted: 11/29/2022] [Indexed: 12/04/2022]  Open
5
Almodaresi F, Khan J, Madaminov S, Ferdman M, Johnson R, Pandey P, Patro R. An incrementally updatable and scalable system for large-scale sequence search using the Bentley-Saxe transformation. Bioinformatics 2022;38:3155-3163. [PMID: 35325039 PMCID: PMC9191210 DOI: 10.1093/bioinformatics/btac142] [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: 06/14/2021] [Revised: 01/10/2022] [Accepted: 03/22/2022] [Indexed: 11/14/2022]  Open
6
Dufault‐Thompson K, Jiang X. Applications of de Bruijn graphs in microbiome research. IMETA 2022;1:e4. [PMID: 38867733 PMCID: PMC10989854 DOI: 10.1002/imt2.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/24/2022] [Accepted: 01/24/2022] [Indexed: 06/14/2024]
7
Břinda K, Baym M, Kucherov G. Simplitigs as an efficient and scalable representation of de Bruijn graphs. Genome Biol 2021;22:96. [PMID: 33823902 PMCID: PMC8025321 DOI: 10.1186/s13059-021-02297-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 02/10/2021] [Indexed: 12/30/2022]  Open
8
Rahman A, Medevedev P. Representation of k-Mer Sets Using Spectrum-Preserving String Sets. J Comput Biol 2021;28:381-394. [PMID: 33290137 PMCID: PMC8066325 DOI: 10.1089/cmb.2020.0431] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
9
Jiang P, Luo J, Wang Y, Deng P, Schmidt B, Tang X, Chen N, Wong L, Zhao L. kmcEx: memory-frugal and retrieval-efficient encoding of counted k-mers. Bioinformatics 2020;35:4871-4878. [PMID: 31038666 DOI: 10.1093/bioinformatics/btz299] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 04/02/2019] [Accepted: 04/19/2019] [Indexed: 12/25/2022]  Open
10
Almodaresi F, Pandey P, Ferdman M, Johnson R, Patro R. An Efficient, Scalable, and Exact Representation of High-Dimensional Color Information Enabled Using de Bruijn Graph Search. J Comput Biol 2020;27:485-499. [PMID: 32176522 PMCID: PMC7185321 DOI: 10.1089/cmb.2019.0322] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
11
Rowe WPM. When the levee breaks: a practical guide to sketching algorithms for processing the flood of genomic data. Genome Biol 2019;20:199. [PMID: 31519212 PMCID: PMC6744645 DOI: 10.1186/s13059-019-1809-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 09/02/2019] [Indexed: 01/21/2023]  Open
12
Marçais G, Solomon B, Patro R, Kingsford C. Sketching and Sublinear Data Structures in Genomics. Annu Rev Biomed Data Sci 2019. [DOI: 10.1146/annurev-biodatasci-072018-021156] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
13
Mustafa H, Schilken I, Karasikov M, Eickhoff C, Rätsch G, Kahles A. Dynamic compression schemes for graph coloring. Bioinformatics 2019;35:407-414. [PMID: 30020403 PMCID: PMC6530811 DOI: 10.1093/bioinformatics/bty632] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 06/22/2018] [Accepted: 07/16/2018] [Indexed: 11/30/2022]  Open
14
Pandey P, Almodaresi F, Bender MA, Ferdman M, Johnson R, Patro R. Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index. Cell Syst 2018;7:201-207.e4. [PMID: 29936185 PMCID: PMC10964368 DOI: 10.1016/j.cels.2018.05.021] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 05/08/2018] [Accepted: 05/25/2018] [Indexed: 01/08/2023]
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