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For: Li H. BFC: correcting Illumina sequencing errors. Bioinformatics 2015;31:2885-7. [PMID: 25953801 DOI: 10.1093/bioinformatics/btv290] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 05/02/2015] [Indexed: 11/12/2022]  Open
Number Cited by Other Article(s)
101
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: 4.8] [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
102
Whole-Genome Sequences of Two Carbapenem-Resistant Klebsiella quasipneumoniae Strains Isolated from a Tertiary Hospital in Johor, Malaysia. GENOME ANNOUNCEMENTS 2017;5:5/32/e00768-17. [PMID: 28798179 PMCID: PMC5552988 DOI: 10.1128/genomea.00768-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
103
Malhotra R, Jha M, Poss M, Acharya R. A random forest classifier for detecting rare variants in NGS data from viral populations. Comput Struct Biotechnol J 2017;15:388-395. [PMID: 28819548 PMCID: PMC5548337 DOI: 10.1016/j.csbj.2017.07.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 07/01/2017] [Accepted: 07/03/2017] [Indexed: 11/28/2022]  Open
104
Dlugosz M, Deorowicz S. RECKONER: read error corrector based on KMC. Bioinformatics 2017;33:1086-1089. [PMID: 28062451 DOI: 10.1093/bioinformatics/btw746] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 11/24/2016] [Indexed: 11/12/2022]  Open
105
Jackman SD, Vandervalk BP, Mohamadi H, Chu J, Yeo S, Hammond SA, Jahesh G, Khan H, Coombe L, Warren RL, Birol I. ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter. Genome Res 2017;27:768-777. [PMID: 28232478 PMCID: PMC5411771 DOI: 10.1101/gr.214346.116] [Citation(s) in RCA: 413] [Impact Index Per Article: 51.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Accepted: 02/14/2017] [Indexed: 01/19/2023]
106
Somervuo P, Yu DW, Xu CC, Ji Y, Hultman J, Wirta H, Ovaskainen O. Quantifying uncertainty of taxonomic placement in DNA barcoding and metabarcoding. Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12721] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
107
Gerhard GS, Bann DV, Broach J, Goldenberg D. Pitfalls of exome sequencing: a case study of the attribution of HABP2 rs7080536 in familial non-medullary thyroid cancer. NPJ Genom Med 2017;2:8. [PMID: 28884020 PMCID: PMC5584869 DOI: 10.1038/s41525-017-0011-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 02/07/2017] [Accepted: 02/28/2017] [Indexed: 02/06/2023]  Open
108
Leray M, Knowlton N. Random sampling causes the low reproducibility of rare eukaryotic OTUs in Illumina COI metabarcoding. PeerJ 2017;5:e3006. [PMID: 28348924 PMCID: PMC5364921 DOI: 10.7717/peerj.3006] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 01/20/2017] [Indexed: 12/15/2022]  Open
109
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: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 02/14/2017] [Indexed: 11/14/2022]  Open
110
Next generation sequencing of gonadal transcriptome suggests standard maternal inheritance of mitochondrial DNA in Eurhomalea rufa (Veneridae). Mar Genomics 2017. [DOI: 10.1016/j.margen.2016.11.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
111
Dolle DD, Liu Z, Cotten M, Simpson JT, Iqbal Z, Durbin R, McCarthy SA, Keane TM. Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes. Genome Res 2016;27:300-309. [PMID: 27986821 PMCID: PMC5287235 DOI: 10.1101/gr.211748.116] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 12/14/2016] [Indexed: 01/04/2023]
112
Gunn L, Finn S, Hurley D, Bai L, Wall E, Iversen C, Threlfall JE, Fanning S. Molecular Characterization of Salmonella Serovars Anatum and Ealing Associated with Two Historical Outbreaks, Linked to Contaminated Powdered Infant Formula. Front Microbiol 2016;7:1664. [PMID: 27818652 PMCID: PMC5073096 DOI: 10.3389/fmicb.2016.01664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 10/05/2016] [Indexed: 11/13/2022]  Open
113
From next-generation resequencing reads to a high-quality variant data set. Heredity (Edinb) 2016;118:111-124. [PMID: 27759079 DOI: 10.1038/hdy.2016.102] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Revised: 09/03/2016] [Accepted: 09/06/2016] [Indexed: 12/11/2022]  Open
114
Hou D, Chen C, Seely EJ, Chen S, Song Y. High-Throughput Sequencing-Based Immune Repertoire Study during Infectious Disease. Front Immunol 2016;7:336. [PMID: 27630639 PMCID: PMC5005336 DOI: 10.3389/fimmu.2016.00336] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 08/19/2016] [Indexed: 11/13/2022]  Open
115
Heo Y, Ramachandran A, Hwu WM, Ma J, Chen D. BLESS 2: accurate, memory-efficient and fast error correction method. ACTA ACUST UNITED AC 2016;32:2369-71. [PMID: 27153708 DOI: 10.1093/bioinformatics/btw146] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 03/12/2016] [Indexed: 11/14/2022]
116
Bremges A, Singer E, Woyke T, Sczyrba A. MeCorS: Metagenome-enabled error correction of single cell sequencing reads. Bioinformatics 2016;32:2199-201. [PMID: 27153586 PMCID: PMC4937190 DOI: 10.1093/bioinformatics/btw144] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Accepted: 03/09/2016] [Indexed: 11/12/2022]  Open
117
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: 2.2] [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
118
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: 190] [Impact Index Per Article: 21.1] [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
119
Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads. Gigascience 2015;4:48. [PMID: 26500767 PMCID: PMC4615873 DOI: 10.1186/s13742-015-0089-y] [Citation(s) in RCA: 329] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 10/09/2015] [Indexed: 11/10/2022]  Open
120
Li H. FermiKit: assembly-based variant calling for Illumina resequencing data. Bioinformatics 2015. [PMID: 26220959 DOI: 10.1093/bioinformatics/btv440] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
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