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For: Molnar M, Ilie L. Correcting Illumina data. Brief Bioinform 2014;16:588-99. [PMID: 25183248 DOI: 10.1093/bib/bbu029] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 08/02/2014] [Indexed: 11/12/2022]  Open
Number Cited by Other Article(s)
1
Sami A, El-Metwally S, Rashad MZ. MAC-ErrorReads: machine learning-assisted classifier for filtering erroneous NGS reads. BMC Bioinformatics 2024;25:61. [PMID: 38321434 PMCID: PMC10848413 DOI: 10.1186/s12859-024-05681-1] [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] [Received: 09/12/2023] [Accepted: 01/29/2024] [Indexed: 02/08/2024]  Open
2
Długosz M, Deorowicz S. Illumina reads correction: evaluation and improvements. Sci Rep 2024;14:2232. [PMID: 38278837 PMCID: PMC11222498 DOI: 10.1038/s41598-024-52386-9] [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] [Received: 03/20/2023] [Accepted: 01/18/2024] [Indexed: 01/28/2024]  Open
3
Heo Y, Manikandan G, Ramachandran A, Chen D. Comprehensive Evaluation of Error-Correction Methodologies for Genome Sequencing Data. Bioinformatics 2021. [DOI: 10.36255/exonpublications.bioinformatics.2021.ch6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
4
Schmeing S, Robinson MD. ReSeq simulates realistic Illumina high-throughput sequencing data. Genome Biol 2021;22:67. [PMID: 33608040 PMCID: PMC7896392 DOI: 10.1186/s13059-021-02265-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 01/07/2021] [Indexed: 12/18/2022]  Open
5
Mitchell K, Brito JJ, Mandric I, Wu Q, Knyazev S, Chang S, Martin LS, Karlsberg A, Gerasimov E, Littman R, Hill BL, Wu NC, Yang HT, Hsieh K, Chen L, Littman E, Shabani T, Enik G, Yao D, Sun R, Schroeder J, Eskin E, Zelikovsky A, Skums P, Pop M, Mangul S. Benchmarking of computational error-correction methods for next-generation sequencing data. Genome Biol 2020;21:71. [PMID: 32183840 PMCID: PMC7079412 DOI: 10.1186/s13059-020-01988-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 03/06/2020] [Indexed: 12/16/2022]  Open
6
Athena: Automated Tuning of k-mer based Genomic Error Correction Algorithms using Language Models. Sci Rep 2019;9:16157. [PMID: 31695060 PMCID: PMC6834855 DOI: 10.1038/s41598-019-52196-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 10/07/2019] [Indexed: 01/30/2023]  Open
7
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: 0.8] [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
8
Heydari M, Miclotte G, Van de Peer Y, Fostier J. Illumina error correction near highly repetitive DNA regions improves de novo genome assembly. BMC Bioinformatics 2019;20:298. [PMID: 31159722 PMCID: PMC6545690 DOI: 10.1186/s12859-019-2906-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/17/2019] [Indexed: 11/10/2022]  Open
9
Zhao L, Xie J, Bai L, Chen W, Wang M, Zhang Z, Wang Y, Zhao Z, Li J. Mining statistically-solid k-mers for accurate NGS error correction. BMC Genomics 2018;19:912. [PMID: 30598110 PMCID: PMC6311904 DOI: 10.1186/s12864-018-5272-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
10
Manekar SC, Sathe SR. A benchmark study of k-mer counting methods for high-throughput sequencing. Gigascience 2018;7:5140149. [PMID: 30346548 PMCID: PMC6280066 DOI: 10.1093/gigascience/giy125] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 10/16/2018] [Indexed: 11/25/2022]  Open
11
Savel D, LaFramboise T, Grama A, Koyuturk M. Pluribus-Exploring the Limits of Error Correction Using a Suffix Tree. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2017;14:1378-1388. [PMID: 27362987 PMCID: PMC5754272 DOI: 10.1109/tcbb.2016.2586060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
12
Large-scale comparative metagenomics of Blastocystis, a common member of the human gut microbiome. ISME JOURNAL 2017;11:2848-2863. [PMID: 28837129 PMCID: PMC5702742 DOI: 10.1038/ismej.2017.139] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 07/05/2017] [Accepted: 07/14/2017] [Indexed: 12/12/2022]
13
Evaluation of the impact of Illumina error correction tools on de novo genome assembly. BMC Bioinformatics 2017;18:374. [PMID: 28821237 PMCID: PMC5563063 DOI: 10.1186/s12859-017-1784-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 08/11/2017] [Indexed: 01/20/2023]  Open
14
Zhao L, Chen Q, Li W, Jiang P, Wong L, Li J. MapReduce for accurate error correction of next-generation sequencing data. Bioinformatics 2017;33:3844-3851. [PMID: 28205674 DOI: 10.1093/bioinformatics/btx089] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 02/14/2017] [Indexed: 11/14/2022]  Open
15
Hershberg U, Luning Prak ET. The analysis of clonal expansions in normal and autoimmune B cell repertoires. Philos Trans R Soc Lond B Biol Sci 2016;370:rstb.2014.0239. [PMID: 26194753 PMCID: PMC4528416 DOI: 10.1098/rstb.2014.0239] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]  Open
16
Sameith K, Roscito JG, Hiller M. Iterative error correction of long sequencing reads maximizes accuracy and improves contig assembly. Brief Bioinform 2016;18:1-8. [PMID: 26868358 PMCID: PMC5221426 DOI: 10.1093/bib/bbw003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 01/02/2016] [Indexed: 11/13/2022]  Open
17
Tong L, Yang C, Wu PY, Wang MD. Evaluating the impact of sequencing error correction for RNA-seq data with ERCC RNA spike-in controls. ... IEEE-EMBS INTERNATIONAL CONFERENCE ON BIOMEDICAL AND HEALTH INFORMATICS. IEEE-EMBS INTERNATIONAL CONFERENCE ON BIOMEDICAL AND HEALTH INFORMATICS 2016;2016:74-77. [PMID: 27532064 DOI: 10.1109/bhi.2016.7455838] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
18
Alic AS, Ruzafa D, Dopazo J, Blanquer I. Objective review ofde novostand-alone error correction methods for NGS data. WILEY INTERDISCIPLINARY REVIEWS: COMPUTATIONAL MOLECULAR SCIENCE 2016. [DOI: 10.1002/wcms.1239] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
19
Laehnemann D, Borkhardt A, McHardy AC. Denoising DNA deep sequencing data-high-throughput sequencing errors and their correction. Brief Bioinform 2016;17:154-79. [PMID: 26026159 PMCID: PMC4719071 DOI: 10.1093/bib/bbv029] [Citation(s) in RCA: 180] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 04/09/2015] [Indexed: 12/23/2022]  Open
20
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: 1.3] [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
21
Marinier E, Brown DG, McConkey BJ. Pollux: platform independent error correction of single and mixed genomes. BMC Bioinformatics 2015;16:10. [PMID: 25592313 PMCID: PMC4307147 DOI: 10.1186/s12859-014-0435-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 12/17/2014] [Indexed: 12/13/2022]  Open
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