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For: 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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 04/09/2015] [Indexed: 12/30/2022]  Open
Number Cited by Other Article(s)
1
Sun H, Zheng Y, Xie H, Ma H, Zhong C, Yan M, Liu X, Wang G. PQSDC: a parallel lossless compressor for quality scores data via sequences partition and run-length prediction mapping. Bioinformatics 2024;40:btae323. [PMID: 38759114 PMCID: PMC11139522 DOI: 10.1093/bioinformatics/btae323] [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: 01/28/2024] [Revised: 04/22/2024] [Accepted: 05/16/2024] [Indexed: 05/19/2024]  Open
2
Chen S, Chen Y, Wang Z, Qin W, Zhang J, Nand H, Zhang J, Li J, Zhang X, Liang X, Xu M. Efficient sequencing data compression and FPGA acceleration based on a two-step framework. Front Genet 2023;14:1260531. [PMID: 37811144 PMCID: PMC10552150 DOI: 10.3389/fgene.2023.1260531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 09/07/2023] [Indexed: 10/10/2023]  Open
3
Liu Y, Shen X, Gong Y, Liu Y, Song B, Zeng X. Sequence Alignment/Map format: a comprehensive review of approaches and applications. Brief Bioinform 2023;24:bbad320. [PMID: 37668049 DOI: 10.1093/bib/bbad320] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/16/2023] [Accepted: 08/18/2023] [Indexed: 09/06/2023]  Open
4
Berger B, Yu YW. Navigating bottlenecks and trade-offs in genomic data analysis. Nat Rev Genet 2023;24:235-250. [PMID: 36476810 PMCID: PMC10204111 DOI: 10.1038/s41576-022-00551-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/27/2022] [Indexed: 12/12/2022]
5
Chen H, Chen J, Lu Z, Wang R. CMIC: an efficient quality score compressor with random access functionality. BMC Bioinformatics 2022;23:294. [PMID: 35870880 PMCID: PMC9308261 DOI: 10.1186/s12859-022-04837-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 07/13/2022] [Indexed: 12/02/2022]  Open
6
Niu Y, Ma M, Li F, Liu X, Shi G. ACO:lossless quality score compression based on adaptive coding order. BMC Bioinformatics 2022;23:219. [PMID: 35672665 PMCID: PMC9175485 DOI: 10.1186/s12859-022-04712-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 04/25/2022] [Indexed: 08/30/2023]  Open
7
Huo H, Liu P, Wang C, Jiang H, Vitter JS. CIndex: compressed indexes for fast retrieval of FASTQ files. Bioinformatics 2022;38:335-343. [PMID: 34524416 DOI: 10.1093/bioinformatics/btab655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 08/12/2021] [Accepted: 09/10/2021] [Indexed: 02/03/2023]  Open
8
Lee D, Song G. FastqCLS: a FASTQ compressor for long-read sequencing via read reordering using a novel scoring model. Bioinformatics 2022;38:351-356. [PMID: 34623374 DOI: 10.1093/bioinformatics/btab696] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 09/29/2021] [Accepted: 10/05/2021] [Indexed: 02/03/2023]  Open
9
Cho M, No A. FCLQC: fast and concurrent lossless quality scores compressor. BMC Bioinformatics 2021;22:606. [PMID: 34930110 PMCID: PMC8686598 DOI: 10.1186/s12859-021-04516-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 12/06/2021] [Indexed: 11/10/2022]  Open
10
Morales VS, Houghten S. Lossy Compression of Quality Values in Sequencing Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021;18:1958-1969. [PMID: 31869798 DOI: 10.1109/tcbb.2019.2959273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
11
Chandak S, Tatwawadi K, Ochoa I, Hernaez M, Weissman T. SPRING: a next-generation compressor for FASTQ data. Bioinformatics 2020;35:2674-2676. [PMID: 30535063 DOI: 10.1093/bioinformatics/bty1015] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 12/06/2018] [Indexed: 01/31/2023]  Open
12
Liu Y, Yu Z, Dinger ME, Li J. Index suffix-prefix overlaps by (w, k)-minimizer to generate long contigs for reads compression. Bioinformatics 2020;35:2066-2074. [PMID: 30407482 DOI: 10.1093/bioinformatics/bty936] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/04/2018] [Accepted: 11/07/2018] [Indexed: 01/23/2023]  Open
13
Fu J, Ke B, Dong S. LCQS: an efficient lossless compression tool of quality scores with random access functionality. BMC Bioinformatics 2020;21:109. [PMID: 32183707 PMCID: PMC7079445 DOI: 10.1186/s12859-020-3428-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 02/24/2020] [Indexed: 12/02/2022]  Open
14
Hernandez-Lopez AA, Alberti C, Mattavelli M. Toward a Dynamic Threshold for Quality Score Distortion in Reference-Based Alignment. J Comput Biol 2020;27:288-300. [PMID: 31891532 DOI: 10.1089/cmb.2019.0333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]  Open
15
FQSqueezer: k-mer-based compression of sequencing data. Sci Rep 2020;10:578. [PMID: 31953467 PMCID: PMC6969201 DOI: 10.1038/s41598-020-57452-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 12/19/2019] [Indexed: 12/26/2022]  Open
16
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]
17
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: 4] [Impact Index Per Article: 0.7] [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
18
Bonfield JK, McCarthy SA, Durbin R. Crumble: reference free lossy compression of sequence quality values. Bioinformatics 2019;35:337-339. [PMID: 29992288 PMCID: PMC6330002 DOI: 10.1093/bioinformatics/bty608] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 07/09/2018] [Indexed: 02/01/2023]  Open
19
Fischer-Hwang I, Ochoa I, Weissman T, Hernaez M. Denoising of Aligned Genomic Data. Sci Rep 2019;9:15067. [PMID: 31636330 PMCID: PMC6803637 DOI: 10.1038/s41598-019-51418-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 09/25/2019] [Indexed: 12/30/2022]  Open
20
Roguski L, Ochoa I, Hernaez M, Deorowicz S. FaStore: a space-saving solution for raw sequencing data. Bioinformatics 2019;34:2748-2756. [PMID: 29617939 DOI: 10.1093/bioinformatics/bty205] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 03/27/2018] [Indexed: 12/29/2022]  Open
21
Hernaez M, Pavlichin D, Weissman T, Ochoa I. Genomic Data Compression. Annu Rev Biomed Data Sci 2019. [DOI: 10.1146/annurev-biodatasci-072018-021229] [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]
22
Yang R, Chen X, Ochoa I. MassComp, a lossless compressor for mass spectrometry data. BMC Bioinformatics 2019;20:368. [PMID: 31262247 PMCID: PMC6604446 DOI: 10.1186/s12859-019-2962-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 06/20/2019] [Indexed: 12/17/2022]  Open
23
Chandak S, Tatwawadi K, Weissman T. Compression of genomic sequencing reads via hash-based reordering: algorithm and analysis. Bioinformatics 2018;34:558-567. [PMID: 29444237 DOI: 10.1093/bioinformatics/btx639] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 10/06/2017] [Indexed: 12/30/2022]  Open
24
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
25
Voges J, Ostermann J, Hernaez M. CALQ: compression of quality values of aligned sequencing data. Bioinformatics 2018;34:1650-1658. [PMID: 29186284 PMCID: PMC5946873 DOI: 10.1093/bioinformatics/btx737] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 10/23/2017] [Accepted: 11/22/2017] [Indexed: 12/30/2022]  Open
26
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
27
Ashley EA. Towards precision medicine. Nat Rev Genet 2017;17:507-22. [PMID: 27528417 DOI: 10.1038/nrg.2016.86] [Citation(s) in RCA: 526] [Impact Index Per Article: 65.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
28
Long R, Hernaez M, Ochoa I, Weissman T. GeneComp, a new reference-based compressor for SAM files. PROCEEDINGS. DATA COMPRESSION CONFERENCE 2017;2017:330-339. [PMID: 29046896 PMCID: PMC5641594 DOI: 10.1109/dcc.2017.76] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
29
Ochoa I, No A, Hernaez M, Weissman T. CROMqs: an infinitesimal successive refinement lossy compressor for the quality scores. PROCEEDINGS. INFORMATION THEORY WORKSHOP 2016;2016:121-125. [PMID: 29806047 DOI: 10.1109/itw.2016.7606808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
30
Greenfield DL, Stegle O, Rrustemi A. GeneCodeq: quality score compression and improved genotyping using a Bayesian framework. Bioinformatics 2016;32:3124-3132. [DOI: 10.1093/bioinformatics/btw385] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 06/15/2016] [Indexed: 12/30/2022]  Open
31
Roguski Ł, Ribeca P. CARGO: effective format-free compressed storage of genomic information. Nucleic Acids Res 2016;44:e114. [PMID: 27131376 PMCID: PMC4937321 DOI: 10.1093/nar/gkw318] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 04/13/2016] [Indexed: 01/21/2023]  Open
32
Ochoa I, Hernaez M, Goldfeder R, Weissman T, Ashley E. Denoising of Quality Scores for Boosted Inference and Reduced Storage. PROCEEDINGS. DATA COMPRESSION CONFERENCE 2016;2016:251-260. [PMID: 29098178 PMCID: PMC5663231 DOI: 10.1109/dcc.2016.92] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
33
Hernaez M, Ochoa I, Weissman T. A cluster-based approach to compression of Quality Scores. PROCEEDINGS. DATA COMPRESSION CONFERENCE 2016;2016:261-270. [PMID: 29057318 DOI: 10.1109/dcc.2016.49] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
34
Alberti C, Daniels N, Hernaez M, Voges J, Goldfeder RL, Hernandez-Lopez AA, Mattavelli M, Berger B. An Evaluation Framework for Lossy Compression of Genome Sequencing Quality Values. PROCEEDINGS. DATA COMPRESSION CONFERENCE 2016;2016:221-230. [PMID: 28845445 PMCID: PMC5568552 DOI: 10.1109/dcc.2016.39] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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