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For: 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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 12/17/2014] [Indexed: 11/14/2022]
Number Cited by Other Article(s)
1
Břinda K, Lima L, Pignotti S, Quinones-Olvera N, Salikhov K, Chikhi R, Kucherov G, Iqbal Z, Baym M. Efficient and robust search of microbial genomes via phylogenetic compression. Nat Methods 2025;22:692-697. [PMID: 40205174 DOI: 10.1038/s41592-025-02625-2] [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: 06/08/2023] [Accepted: 02/12/2025] [Indexed: 04/11/2025]
2
Kowalski TM, Grabowski S. PgRC2: engineering the compression of sequencing reads. Bioinformatics 2025;41:btaf101. [PMID: 40037801 PMCID: PMC11908645 DOI: 10.1093/bioinformatics/btaf101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2024] [Revised: 01/23/2025] [Accepted: 02/28/2025] [Indexed: 03/06/2025]  Open
3
Zheng H, Marçais G, Kingsford C. Creating and Using Minimizer Sketches in Computational Genomics. J Comput Biol 2023;30:1251-1276. [PMID: 37646787 PMCID: PMC11082048 DOI: 10.1089/cmb.2023.0094] [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] [Indexed: 09/01/2023]  Open
4
Sun H, Zheng Y, Xie H, Ma H, Liu X, Wang G. PMFFRC: a large-scale genomic short reads compression optimizer via memory modeling and redundant clustering. BMC Bioinformatics 2023;24:454. [PMID: 38036969 PMCID: PMC10691058 DOI: 10.1186/s12859-023-05566-9] [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: 09/12/2023] [Accepted: 11/13/2023] [Indexed: 12/02/2023]  Open
5
Tang T, Hutvagner G, Wang W, Li J. Simultaneous compression of multiple error-corrected short-read sets for faster data transmission and better de novo assemblies. Brief Funct Genomics 2022;21:387-398. [PMID: 35848773 DOI: 10.1093/bfgp/elac016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 06/10/2022] [Accepted: 06/14/2022] [Indexed: 11/14/2022]  Open
6
CoLoRd: compressing long reads. Nat Methods 2022;19:441-444. [PMID: 35347321 DOI: 10.1038/s41592-022-01432-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 02/23/2022] [Indexed: 01/30/2023]
7
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
8
Liu Y, Zhang X, Zou Q, Zeng X. Minirmd: accurate and fast duplicate removal tool for short reads via multiple minimizers. Bioinformatics 2021;37:1604-1606. [PMID: 33112385 DOI: 10.1093/bioinformatics/btaa915] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/30/2020] [Accepted: 10/14/2020] [Indexed: 12/21/2022]  Open
9
Liu Y, Li J. Hamming-shifting graph of genomic short reads: Efficient construction and its application for compression. PLoS Comput Biol 2021;17:e1009229. [PMID: 34280186 PMCID: PMC8321399 DOI: 10.1371/journal.pcbi.1009229] [Citation(s) in RCA: 8] [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: 01/06/2021] [Revised: 07/29/2021] [Accepted: 06/30/2021] [Indexed: 11/21/2022]  Open
10
Tang T, Li J. Transformation of FASTA files into feature vectors for unsupervised compression of short reads databases. J Bioinform Comput Biol 2021;19:2050048. [PMID: 33472569 DOI: 10.1142/s0219720020500481] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
11
Holley G, Melsted P. Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs. Genome Biol 2020;21:249. [PMID: 32943081 PMCID: PMC7499882 DOI: 10.1186/s13059-020-02135-8] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 08/06/2020] [Indexed: 02/07/2023]  Open
12
Kowalski TM, Grabowski S. PgRC: pseudogenome-based read compressor. Bioinformatics 2020;36:2082-2089. [PMID: 31893286 DOI: 10.1093/bioinformatics/btz919] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 11/28/2019] [Accepted: 12/05/2019] [Indexed: 01/26/2023]  Open
13
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
14
Kockan C, Zhu K, Dokmai N, Karpov N, Kulekci MO, Woodruff DP, Sahinalp SC. Sketching algorithms for genomic data analysis and querying in a secure enclave. Nat Methods 2020;17:295-301. [PMID: 32132732 DOI: 10.1038/s41592-020-0761-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 01/22/2020] [Indexed: 11/09/2022]
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. 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
17
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
18
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]
19
Guerra A, Lotero J, Aedo JÉ, Isaza S. Tackling the Challenges of FASTQ Referential Compression. Bioinform Biol Insights 2019;13:1177932218821373. [PMID: 30792576 PMCID: PMC6376532 DOI: 10.1177/1177932218821373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 11/26/2018] [Indexed: 11/16/2022]  Open
20
Sardaraz M, Tahir M. FCompress: An Algorithm for FASTQ Sequence Data Compression. Curr Bioinform 2019. [DOI: 10.2174/1574893613666180322125337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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
Wang R, Li J, Bai Y, Zang T, Wang Y. BdBG: a bucket-based method for compressing genome sequencing data with dynamic de Bruijn graphs. PeerJ 2018;6:e5611. [PMID: 30364599 PMCID: PMC6197042 DOI: 10.7717/peerj.5611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 09/13/2018] [Indexed: 02/01/2023]  Open
23
Holley G, Wittler R, Stoye J, Hach F. Dynamic Alignment-Free and Reference-Free Read Compression. J Comput Biol 2018;25:825-836. [PMID: 30011247 DOI: 10.1089/cmb.2018.0068] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
24
Optimal compressed representation of high throughput sequence data via light assembly. Nat Commun 2018;9:566. [PMID: 29422526 PMCID: PMC5805770 DOI: 10.1038/s41467-017-02480-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Accepted: 12/05/2017] [Indexed: 12/21/2022]  Open
25
Huang ZA, Wen Z, Deng Q, Chu Y, Sun Y, Zhu Z. LW-FQZip 2: a parallelized reference-based compression of FASTQ files. BMC Bioinformatics 2017;18:179. [PMID: 28320326 PMCID: PMC5359991 DOI: 10.1186/s12859-017-1588-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Accepted: 03/09/2017] [Indexed: 01/06/2023]  Open
26
Paridaens T, Van Wallendael G, De Neve W, Lambert P. AFRESh: an adaptive framework for compression of reads and assembled sequences with random access functionality. Bioinformatics 2017;33:1464-1472. [DOI: 10.1093/bioinformatics/btx001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 01/03/2017] [Indexed: 11/14/2022]  Open
27
Holley G, Wittler R, Stoye J, Hach F. Dynamic Alignment-Free and Reference-Free Read Compression. LECTURE NOTES IN COMPUTER SCIENCE 2017. [DOI: 10.1007/978-3-319-56970-3_4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
28
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
29
Comparison of high-throughput sequencing data compression tools. Nat Methods 2016;13:1005-1008. [PMID: 27776113 DOI: 10.1038/nmeth.4037] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 09/01/2016] [Indexed: 12/27/2022]
30
A Survey on Data Compression Methods for Biological Sequences. INFORMATION 2016. [DOI: 10.3390/info7040056] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]  Open
31
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
32
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
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
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
35
Kowalski T, Grabowski S, Deorowicz S. Indexing Arbitrary-Length k-Mers in Sequencing Reads. PLoS One 2015;10:e0133198. [PMID: 26182400 PMCID: PMC4504488 DOI: 10.1371/journal.pone.0133198] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 06/24/2015] [Indexed: 11/25/2022]  Open
36
Deorowicz S, Danek A, Niemiec M. GDC 2: Compression of large collections of genomes. Sci Rep 2015;5:11565. [PMID: 26108279 PMCID: PMC4479802 DOI: 10.1038/srep11565] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/28/2015] [Indexed: 01/18/2023]  Open
37
Sampling the Suffix Array with Minimizers. STRING PROCESSING AND INFORMATION RETRIEVAL 2015. [DOI: 10.1007/978-3-319-23826-5_28] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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