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For: Salmela L, Rivals E. LoRDEC: accurate and efficient long read error correction. ACTA ACUST UNITED AC 2014;30:3506-14. [PMID: 25165095 PMCID: PMC4253826 DOI: 10.1093/bioinformatics/btu538] [Citation(s) in RCA: 476] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Number Cited by Other Article(s)
451
Weirather JL, de Cesare M, Wang Y, Piazza P, Sebastiano V, Wang XJ, Buck D, Au KF. Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis. F1000Res 2017;6:100. [PMID: 28868132 PMCID: PMC5553090 DOI: 10.12688/f1000research.10571.1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/09/2017] [Indexed: 09/05/2023]  Open
452
Weirather JL, de Cesare M, Wang Y, Piazza P, Sebastiano V, Wang XJ, Buck D, Au KF. Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis. F1000Res 2017;6:100. [PMID: 28868132 PMCID: PMC5553090 DOI: 10.12688/f1000research.10571.2] [Citation(s) in RCA: 281] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/09/2017] [Indexed: 12/11/2022]  Open
453
Complex modular architecture around a simple toolkit of wing pattern genes. Nat Ecol Evol 2017;1:52. [PMID: 28523290 DOI: 10.1038/s41559-016-0052] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
454
Zimin AV, Puiu D, Luo MC, Zhu T, Koren S, Marçais G, Yorke JA, Dvořák J, Salzberg SL. Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm. Genome Res 2017;27:787-792. [PMID: 28130360 PMCID: PMC5411773 DOI: 10.1101/gr.213405.116] [Citation(s) in RCA: 274] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 01/18/2017] [Indexed: 01/12/2023]
455
Hu R, Sun G, Sun X. LSCplus: a fast solution for improving long read accuracy by short read alignment. BMC Bioinformatics 2016;17:451. [PMID: 27829364 PMCID: PMC5103424 DOI: 10.1186/s12859-016-1316-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 10/27/2016] [Indexed: 11/10/2022]  Open
456
DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies. Sci Rep 2016;6:31900. [PMID: 27573208 PMCID: PMC5004134 DOI: 10.1038/srep31900] [Citation(s) in RCA: 203] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 07/20/2016] [Indexed: 11/08/2022]  Open
457
Escalona M, Rocha S, Posada D. A comparison of tools for the simulation of genomic next-generation sequencing data. Nat Rev Genet 2016;17:459-69. [PMID: 27320129 PMCID: PMC5224698 DOI: 10.1038/nrg.2016.57] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
458
Chakraborty M, Baldwin-Brown JG, Long AD, Emerson JJ. Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage. Nucleic Acids Res 2016;44:e147. [PMID: 27458204 PMCID: PMC5100563 DOI: 10.1093/nar/gkw654] [Citation(s) in RCA: 230] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 07/09/2016] [Indexed: 01/19/2023]  Open
459
Krishnan NM, Jain P, Gupta S, Hariharan AK, Panda B. An Improved Genome Assembly of Azadirachta indica A. Juss. G3 (BETHESDA, MD.) 2016. [PMID: 27172223 DOI: 10.1534/g1533.1116.030056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
460
An Improved Genome Assembly of Azadirachta indica A. Juss. G3-GENES GENOMES GENETICS 2016;6:1835-40. [PMID: 27172223 PMCID: PMC4938638 DOI: 10.1534/g3.116.030056] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
461
Abdel-Ghany SE, Hamilton M, Jacobi JL, Ngam P, Devitt N, Schilkey F, Ben-Hur A, Reddy ASN. A survey of the sorghum transcriptome using single-molecule long reads. Nat Commun 2016;7:11706. [PMID: 27339290 PMCID: PMC4931028 DOI: 10.1038/ncomms11706] [Citation(s) in RCA: 349] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 04/20/2016] [Indexed: 12/31/2022]  Open
462
Limasset A, Cazaux B, Rivals E, Peterlongo P. Read mapping on de Bruijn graphs. BMC Bioinformatics 2016;17:237. [PMID: 27306641 PMCID: PMC4910249 DOI: 10.1186/s12859-016-1103-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 05/26/2016] [Indexed: 11/10/2022]  Open
463
Ye C, Ma ZS. Sparc: a sparsity-based consensus algorithm for long erroneous sequencing reads. PeerJ 2016;4:e2016. [PMID: 27330851 PMCID: PMC4906657 DOI: 10.7717/peerj.2016] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 04/15/2016] [Indexed: 11/20/2022]  Open
464
Kilgore MB, Kutchan TM. The Amaryllidaceae alkaloids: biosynthesis and methods for enzyme discovery. PHYTOCHEMISTRY REVIEWS : PROCEEDINGS OF THE PHYTOCHEMICAL SOCIETY OF EUROPE 2016;15:317-337. [PMID: 27340382 PMCID: PMC4914137 DOI: 10.1007/s11101-015-9451-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 12/08/2015] [Indexed: 05/21/2023]
465
Miclotte G, Heydari M, Demeester P, Rombauts S, Van de Peer Y, Audenaert P, Fostier J. Jabba: hybrid error correction for long sequencing reads. Algorithms Mol Biol 2016;11:10. [PMID: 27148393 PMCID: PMC4855726 DOI: 10.1186/s13015-016-0075-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 04/25/2016] [Indexed: 11/13/2022]  Open
466
Le Bras Y, Collin O, Monjeaud C, Lacroix V, Rivals É, Lemaitre C, Miele V, Sacomoto G, Marchet C, Cazaux B, Zine El Aabidine A, Salmela L, Alves-Carvalho S, Andrieux A, Uricaru R, Peterlongo P. Colib'read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads. Gigascience 2016;5:9. [PMID: 26870323 PMCID: PMC4750246 DOI: 10.1186/s13742-015-0105-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 12/07/2015] [Indexed: 02/05/2023]  Open
467
Bankevich A, Pevzner PA. TruSPAdes: barcode assembly of TruSeq synthetic long reads. Nat Methods 2016;13:248-50. [PMID: 26828418 DOI: 10.1038/nmeth.3737] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 12/08/2015] [Indexed: 01/12/2023]
468
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: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
469
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
470
Dong L, Liu H, Zhang J, Yang S, Kong G, Chu JSC, Chen N, Wang D. Single-molecule real-time transcript sequencing facilitates common wheat genome annotation and grain transcriptome research. BMC Genomics 2015;16:1039. [PMID: 26645802 PMCID: PMC4673716 DOI: 10.1186/s12864-015-2257-y] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 11/30/2015] [Indexed: 11/25/2022]  Open
471
Lin HH, Liao YC. Evaluation and Validation of Assembling Corrected PacBio Long Reads for Microbial Genome Completion via Hybrid Approaches. PLoS One 2015;10:e0144305. [PMID: 26641475 PMCID: PMC4671558 DOI: 10.1371/journal.pone.0144305] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 11/16/2015] [Indexed: 11/23/2022]  Open
472
Fertin G, Jean G, Radulescu A, Rusu I. Hybrid de novo tandem repeat detection using short and long reads. BMC Med Genomics 2015;8 Suppl 3:S5. [PMID: 26399998 PMCID: PMC4582210 DOI: 10.1186/1755-8794-8-s3-s5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]  Open
473
Allam A, Kalnis P, Solovyev V. Karect: accurate correction of substitution, insertion and deletion errors for next-generation sequencing data. Bioinformatics 2015;31:3421-8. [DOI: 10.1093/bioinformatics/btv415] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 07/08/2015] [Indexed: 11/12/2022]  Open
474
Madoui MA, Engelen S, Cruaud C, Belser C, Bertrand L, Alberti A, Lemainque A, Wincker P, Aury JM. Genome assembly using Nanopore-guided long and error-free DNA reads. BMC Genomics 2015;16:327. [PMID: 25927464 PMCID: PMC4460631 DOI: 10.1186/s12864-015-1519-z] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 04/10/2015] [Indexed: 11/10/2022]  Open
475
Utturkar SM, Klingeman DM, Bruno-Barcena JM, Chinn MS, Grunden AM, Köpke M, Brown SD. Sequence data for Clostridium autoethanogenum using three generations of sequencing technologies. Sci Data 2015;2:150014. [PMID: 25977818 PMCID: PMC4409012 DOI: 10.1038/sdata.2015.14] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 03/12/2015] [Indexed: 01/07/2023]  Open
476
One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly. Curr Opin Microbiol 2014;23:110-20. [PMID: 25461581 DOI: 10.1016/j.mib.2014.11.014] [Citation(s) in RCA: 274] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 11/17/2014] [Accepted: 11/18/2014] [Indexed: 11/20/2022]
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