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Number Cited by Other Article(s)
1
No A, Hernaez M, Ochoa I. CROMqs: An infinitesimal successive refinement lossy compressor for the quality scores. J Bioinform Comput Biol 2020;18:2050031. [PMID: 32938284 DOI: 10.1142/s0219720020500316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
2
Guerrini V, Louza FA, Rosone G. Metagenomic analysis through the extended Burrows-Wheeler transform. BMC Bioinformatics 2020;21:299. [PMID: 32938362 PMCID: PMC7493373 DOI: 10.1186/s12859-020-03628-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 06/22/2020] [Indexed: 11/10/2022]  Open
3
Prezza N, Pisanti N, Sciortino M, Rosone G. Variable-order reference-free variant discovery with the Burrows-Wheeler Transform. BMC Bioinformatics 2020;21:260. [PMID: 32938358 PMCID: PMC7493873 DOI: 10.1186/s12859-020-03586-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 06/08/2020] [Indexed: 11/10/2022]  Open
4
Shibuya Y, Comin M. Indexing k-mers in linear space for quality value compression. J Bioinform Comput Biol 2019;17:1940011. [DOI: 10.1142/s0219720019400110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
5
Shibuya Y, Comin M. Better quality score compression through sequence-based quality smoothing. BMC Bioinformatics 2019;20:302. [PMID: 31757199 PMCID: PMC6873394 DOI: 10.1186/s12859-019-2883-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 05/07/2019] [Indexed: 11/10/2022]  Open
6
Kimura K, Koike A. Parallel Computation of the Burrows-Wheeler Transform of Short Reads Using Prefix Parallelism. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019;16:3-13. [PMID: 29994538 DOI: 10.1109/tcbb.2018.2837749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
7
Voges J, Fotouhi A, Ostermann J, Külekci MO. A Two-Level Scheme for Quality Score Compression. J Comput Biol 2018;25:1141-1151. [PMID: 30059248 DOI: 10.1089/cmb.2018.0065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]  Open
8
Ochoa I, Hernaez M, Goldfeder R, Weissman T, Ashley E. Effect of lossy compression of quality scores on variant calling. Brief Bioinform 2017;18:183-194. [PMID: 26966283 DOI: 10.1093/bib/bbw011] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Indexed: 12/30/2022]  Open
9
Kimura K, Koike A. Analysis of genomic rearrangements by using the Burrows-Wheeler transform of short-read data. BMC Bioinformatics 2015;16 Suppl 18:S5. [PMID: 26678411 PMCID: PMC4708002 DOI: 10.1186/1471-2105-16-s18-s5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]  Open
10
Wandelt S, Leser U. Sequence Factorization with Multiple References. PLoS One 2015;10:e0139000. [PMID: 26422374 PMCID: PMC4589410 DOI: 10.1371/journal.pone.0139000] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 09/07/2015] [Indexed: 11/29/2022]  Open
11
Benoit G, Lemaitre C, Lavenier D, Drezen E, Dayris T, Uricaru R, Rizk G. Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph. BMC Bioinformatics 2015;16:288. [PMID: 26370285 PMCID: PMC4570262 DOI: 10.1186/s12859-015-0709-7] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 08/17/2015] [Indexed: 01/09/2023]  Open
12
Zhang Y, Li L, Yang Y, Yang X, He S, Zhu Z. Light-weight reference-based compression of FASTQ data. BMC Bioinformatics 2015;16:188. [PMID: 26051252 PMCID: PMC4459677 DOI: 10.1186/s12859-015-0628-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 05/27/2015] [Indexed: 01/23/2023]  Open
13
Malysa G, Hernaez M, Ochoa I, Rao M, Ganesan K, Weissman T. QVZ: lossy compression of quality values. Bioinformatics 2015;31:3122-9. [PMID: 26026138 DOI: 10.1093/bioinformatics/btv330] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 04/09/2015] [Indexed: 12/30/2022]  Open
14
Yu YW, Yorukoglu D, Peng J, Berger B. Quality score compression improves genotyping accuracy. Nat Biotechnol 2015;33:240-3. [PMID: 25748910 PMCID: PMC4439189 DOI: 10.1038/nbt.3170] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
15
Grabowski S, Deorowicz S, Roguski Ł. Disk-based compression of data from genome sequencing. ACTA ACUST UNITED AC 2014;31:1389-95. [PMID: 25536966 DOI: 10.1093/bioinformatics/btu844] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 12/17/2014] [Indexed: 11/14/2022]
16
Zhou J, Ji Z, Zhu Z, He S. Compression of next-generation sequencing quality scores using memetic algorithm. BMC Bioinformatics 2014;15 Suppl 15:S10. [PMID: 25474747 PMCID: PMC4271560 DOI: 10.1186/1471-2105-15-s15-s10] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]  Open
17
Holt J, McMillan L. Merging of multi-string BWTs with applications. Bioinformatics 2014;30:3524-31. [PMID: 25172922 DOI: 10.1093/bioinformatics/btu584] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
18
Janin L, Schulz-Trieglaff O, Cox AJ. BEETL-fastq: a searchable compressed archive for DNA reads. Bioinformatics 2014;30:2796-801. [PMID: 24950811 DOI: 10.1093/bioinformatics/btu387] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]  Open
19
Cánovas R, Moffat A, Turpin A. Lossy compression of quality scores in genomic data. Bioinformatics 2014;30:2130-6. [DOI: 10.1093/bioinformatics/btu183] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
20
Yu YW, Yorukoglu D, Berger B. Traversing the k-mer Landscape of NGS Read Datasets for Quality Score Sparsification. RESEARCH IN COMPUTATIONAL MOLECULAR BIOLOGY : ... ANNUAL INTERNATIONAL CONFERENCE, RECOMB ... : PROCEEDINGS. RECOMB (CONFERENCE : 2005- ) 2014;8394:385-399. [PMID: 28825060 DOI: 10.1007/978-3-319-05269-4_31] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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