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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
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
5
Rivara-Espasandín M, Balestrazzi L, Dufort y Álvarez G, Ochoa I, Seroussi G, Smircich P, Sotelo-Silveira J, Martín Á. Nanopore quality score resolution can be reduced with little effect on downstream analysis. BIOINFORMATICS ADVANCES 2022;2:vbac054. [PMID: 36699360 PMCID: PMC9710687 DOI: 10.1093/bioadv/vbac054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 07/13/2022] [Accepted: 08/08/2022] [Indexed: 01/28/2023]
6
Bonfield JK. CRAM 3.1: advances in the CRAM file format. Bioinformatics 2022;38:1497-1503. [PMID: 34999766 PMCID: PMC8896640 DOI: 10.1093/bioinformatics/btac010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/14/2021] [Accepted: 01/04/2022] [Indexed: 02/04/2023]  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
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]
10
Yu R, Yang W, Wang S. Performance evaluation of lossy quality compression algorithms for RNA-seq data. BMC Bioinformatics 2020;21:321. [PMID: 32689929 PMCID: PMC7372835 DOI: 10.1186/s12859-020-03658-4] [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: 05/21/2020] [Accepted: 07/13/2020] [Indexed: 11/29/2022]  Open
11
Yu R, Yang W. ScaleQC: a scalable lossy to lossless solution for NGS data compression. Bioinformatics 2020;36:4551-4559. [DOI: 10.1093/bioinformatics/btaa543] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 04/25/2020] [Accepted: 05/20/2020] [Indexed: 12/30/2022]  Open
12
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]
13
Shokrof M, Abouelhoda M. IonCRAM: a reference-based compression tool for ion torrent sequence files. BMC Bioinformatics 2020;21:397. [PMID: 32907531 PMCID: PMC7487613 DOI: 10.1186/s12859-020-03726-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 08/31/2020] [Indexed: 12/29/2022]  Open
14
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
15
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
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
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]
21
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
22
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
23
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
24
Paridaens T, Van Wallendael G, De Neve W, Lambert P. AQUa: an adaptive framework for compression of sequencing quality scores with random access functionality. Bioinformatics 2018;34:425-433. [PMID: 29028894 DOI: 10.1093/bioinformatics/btx607] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 09/22/2017] [Indexed: 01/09/2023]  Open
25
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
26
Sarkar H, Patro R. Quark enables semi-reference-based compression of RNA-seq data. Bioinformatics 2017;33:3380-3386. [DOI: 10.1093/bioinformatics/btx428] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Accepted: 06/29/2017] [Indexed: 12/19/2022]  Open
27
Cánovas R, Moffat A, Turpin A. CSAM: Compressed SAM format. Bioinformatics 2016;32:3709-3716. [PMID: 27540265 DOI: 10.1093/bioinformatics/btw543] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 08/13/2016] [Accepted: 08/15/2016] [Indexed: 11/13/2022]  Open
28
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]
29
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
30
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]
31
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]
32
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]
33
Sardaraz M, Tahir M, Ikram AA. Advances in high throughput DNA sequence data compression. J Bioinform Comput Biol 2015;14:1630002. [PMID: 26846812 DOI: 10.1142/s0219720016300021] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
34
Xie X, Zhou S, Guan J. CoGI: Towards Compressing Genomes as an Image. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2015;12:1275-1285. [PMID: 26671800 DOI: 10.1109/tcbb.2015.2430331] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
35
Ochoa I, Hernaez M, Weissman T. Aligned genomic data compression via improved modeling. J Bioinform Comput Biol 2015;12:1442002. [PMID: 25395305 DOI: 10.1142/s0219720014420025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
36
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: 45] [Impact Index Per Article: 4.5] [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
37
Patro R, Kingsford C. Data-dependent bucketing improves reference-free compression of sequencing reads. Bioinformatics 2015;31:2770-7. [PMID: 25910696 PMCID: PMC4547610 DOI: 10.1093/bioinformatics/btv248] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Revised: 04/11/2015] [Accepted: 04/20/2015] [Indexed: 01/24/2023]  Open
38
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
39
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]
40
Kingsford C, Patro R. Reference-based compression of short-read sequences using path encoding. Bioinformatics 2015;31:1920-8. [PMID: 25649622 PMCID: PMC4481695 DOI: 10.1093/bioinformatics/btv071] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 01/29/2015] [Indexed: 12/31/2022]  Open
41
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: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 12/17/2014] [Indexed: 11/14/2022]
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