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For: Firtina C, Park J, Alser M, Kim JS, Cali D, Shahroodi T, Ghiasi N, Singh G, Kanellopoulos K, Alkan C, Mutlu O. BLEND: a fast, memory-efficient and accurate mechanism to find fuzzy seed matches in genome analysis. NAR Genom Bioinform 2023;5:lqad004. [PMID: 36685727 PMCID: PMC9853099 DOI: 10.1093/nargab/lqad004] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 12/16/2022] [Accepted: 01/10/2023] [Indexed: 01/22/2023]  Open
Number Cited by Other Article(s)
1
Kong T, Wang Y, Liu B. xRead: a coverage-guided approach for scalable construction of read overlapping graph. Gigascience 2025;14:giaf007. [PMID: 39960665 PMCID: PMC11831799 DOI: 10.1093/gigascience/giaf007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 11/29/2024] [Accepted: 01/10/2025] [Indexed: 02/20/2025]  Open
2
Cavlak MB, Singh G, Alser M, Firtina C, Lindegger J, Sadrosadati M, Mansouri Ghiasi N, Alkan C, Mutlu O. TargetCall: eliminating the wasted computation in basecalling via pre-basecalling filtering. Front Genet 2024;15:1429306. [PMID: 39529848 PMCID: PMC11551021 DOI: 10.3389/fgene.2024.1429306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 09/30/2024] [Indexed: 11/16/2024]  Open
3
Baudeau T, Sahlin K. Improved sub-genomic RNA prediction with the ARTIC protocol. Nucleic Acids Res 2024;52:e82. [PMID: 39149898 PMCID: PMC11417393 DOI: 10.1093/nar/gkae687] [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: 09/21/2023] [Revised: 07/18/2024] [Accepted: 07/25/2024] [Indexed: 08/17/2024]  Open
4
Sharma GK, Sharma R, Joshi K, Qureshi S, Mathur S, Sinha S, Chatterjee S, Nunia V. Advancing microbial diagnostics: a universal phylogeny guided computational algorithm to find unique sequences for precise microorganism detection. Brief Bioinform 2024;25:bbae545. [PMID: 39441245 PMCID: PMC11497845 DOI: 10.1093/bib/bbae545] [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: 01/06/2024] [Revised: 09/21/2024] [Accepted: 10/11/2024] [Indexed: 10/25/2024]  Open
5
Wang S, Jiang Y, Che L, Wang RH, Li SC. Enhancing insights into diseases through horizontal gene transfer event detection from gut microbiome. Nucleic Acids Res 2024;52:e61. [PMID: 38884260 DOI: 10.1093/nar/gkae515] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 04/23/2024] [Accepted: 06/04/2024] [Indexed: 06/18/2024]  Open
6
Firtina C, Soysal M, Lindegger J, Mutlu O. RawHash2: mapping raw nanopore signals using hash-based seeding and adaptive quantization. Bioinformatics 2024;40:btae478. [PMID: 39078113 PMCID: PMC11333567 DOI: 10.1093/bioinformatics/btae478] [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: 11/03/2023] [Revised: 07/04/2024] [Accepted: 07/29/2024] [Indexed: 07/31/2024]  Open
7
Xu W, Hsu PK, Moshiri N, Yu S, Rosing T. HyperGen: Compact and Efficient Genome Sketching using Hyperdimensional Vectors. Bioinformatics 2024;40:btae452. [PMID: 39012512 PMCID: PMC11281827 DOI: 10.1093/bioinformatics/btae452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 07/09/2024] [Accepted: 07/12/2024] [Indexed: 07/17/2024]  Open
8
Karami M, Soltani Mohammadi A, Martin M, Ekim B, Shen W, Guo L, Xu M, Pibiri GE, Patro R, Sahlin K. Designing efficient randstrobes for sequence similarity analyses. Bioinformatics 2024;40:btae187. [PMID: 38579261 PMCID: PMC11034988 DOI: 10.1093/bioinformatics/btae187] [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: 10/18/2023] [Revised: 02/23/2024] [Accepted: 04/04/2024] [Indexed: 04/07/2024]  Open
9
Greenberg G, Ravi AN, Shomorony I. LexicHash: sequence similarity estimation via lexicographic comparison of hashes. Bioinformatics 2023;39:btad652. [PMID: 37878809 PMCID: PMC10628434 DOI: 10.1093/bioinformatics/btad652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 10/11/2023] [Accepted: 10/23/2023] [Indexed: 10/27/2023]  Open
10
Kille B, Garrison E, Treangen TJ, Phillippy AM. Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation. Bioinformatics 2023;39:btad512. [PMID: 37603771 PMCID: PMC10505501 DOI: 10.1093/bioinformatics/btad512] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/19/2023] [Accepted: 08/18/2023] [Indexed: 08/23/2023]  Open
11
Ayad LAK, Chikhi R, Pissis SP. Seedability: optimizing alignment parameters for sensitive sequence comparison. BIOINFORMATICS ADVANCES 2023;3:vbad108. [PMID: 37621456 PMCID: PMC10444664 DOI: 10.1093/bioadv/vbad108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 08/02/2023] [Accepted: 08/10/2023] [Indexed: 08/26/2023]
12
Ekim B, Sahlin K, Medvedev P, Berger B, Chikhi R. Efficient mapping of accurate long reads in minimizer space with mapquik. Genome Res 2023;33:1188-1197. [PMID: 37399256 PMCID: PMC10538364 DOI: 10.1101/gr.277679.123] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 06/26/2023] [Indexed: 07/05/2023]
13
Maier BD, Sahlin K. Entropy predicts sensitivity of pseudorandom seeds. Genome Res 2023;33:1162-1174. [PMID: 37217253 PMCID: PMC10538493 DOI: 10.1101/gr.277645.123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 05/04/2023] [Indexed: 05/24/2023]
14
Firtina C, Mansouri Ghiasi N, Lindegger J, Singh G, Cavlak MB, Mao H, Mutlu O. RawHash: enabling fast and accurate real-time analysis of raw nanopore signals for large genomes. Bioinformatics 2023;39:i297-i307. [PMID: 37387139 PMCID: PMC10311405 DOI: 10.1093/bioinformatics/btad272] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]  Open
15
Sahlin K, Baudeau T, Cazaux B, Marchet C. A survey of mapping algorithms in the long-reads era. Genome Biol 2023;24:133. [PMID: 37264447 PMCID: PMC10236595 DOI: 10.1186/s13059-023-02972-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 05/12/2023] [Indexed: 06/03/2023]  Open
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