title: Improving transcriptome assembly through error correction of high-throughput sequence reads.
abstract: The study of functional genomics, particularly in non-model organisms, has been dramatically improved over the last few years by the use of transcriptomes and RNAseq. While these studies are potentially extremely powerful, a computationally intensive procedure, the de novo construction of a reference transcriptome must be completed as a prerequisite to further analyses. The accurate reference is critically important as all downstream steps, including estimating transcript abundance are critically dependent on the construction of an accurate reference. Though a substantial amount of research has been done on assembly, only recently have the pre-assembly procedures been studied in detail. Specifically, several stand-alone error correction modules have been reported on and, while they have shown to be effective in reducing errors at the level of sequencing reads, how error correction impacts assembly accuracy is largely unknown. Here, we show via use of a simulated and empiric dataset, that applying error correction to sequencing reads has significant positive effects on assembly accuracy, and should be applied to all datasets. A complete collection of commands which will allow for the production of Reptile corrected reads is available at https://github.com/macmanes/error_correction/tree/master/scripts and as File S1.
authors.affiliation: California Institute for Quantitative Biosciences, University of California , Berkeley, CA , USA.
authors.forename: Matthew D
authors.initials: MD
authors.lastname: Macmanes
authors.forename: Michael B
authors.initials: MB
authors.lastname: Eisen
keywords: De novo assembly; Error correction; Illumina; RNAseq; Trinity
references.citation: Mol Ecol. 2013 Jun;22(11):3090-7
references.pmid: 23452191
references.citation: Bioinformatics. 2010 Jun 15;26(12):i367-73
references.pmid: 20529929
references.citation: Nat Biotechnol. 2011 May 15;29(7):644-52
references.pmid: 21572440
references.citation: Mol Ecol. 2013 Feb;22(3):620-34
references.pmid: 22998089
references.citation: BMC Bioinformatics. 2010 Sep 27;11:485
references.pmid: 20875133
references.citation: Bioinformatics. 2012 Nov 15;28(22):2870-4
references.pmid: 23044551
references.citation: Proc Natl Acad Sci U S A. 2012 Aug 14;109(33):13272-7
references.pmid: 22847406
references.citation: Genome Res. 2011 Dec;21(12):2224-41
references.pmid: 21926179
references.citation: BMC Bioinformatics. 2013 Mar 09;14:91
references.pmid: 23497356
references.citation: Nucleic Acids Res. 2013 May 1;41(10):e109
references.pmid: 23558750
references.citation: Bioinformatics. 2010 Oct 15;26(20):2526-33
references.pmid: 20834037
references.citation: Bioinformatics. 2011 Feb 15;27(4):479-86
references.pmid: 21245053
references.citation: BMC Bioinformatics. 2009 Dec 15;10:421
references.pmid: 20003500
references.citation: Nat Biotechnol. 2010 May;28(5):511-5
references.pmid: 20436464
references.citation: Bioinformatics. 2009 Apr 15;25(8):1026-32
references.pmid: 19244387
references.citation: BMC Syst Biol. 2011;5 Suppl 3:S1
references.pmid: 22784615
references.citation: Genome Res. 2011 Jul;21(7):1181-92
references.pmid: 21482625
references.citation: PLoS One. 2012;7(8):e40950
references.pmid: 22879883
references.citation: Brief Bioinform. 2013 Jan;14(1):56-66
references.pmid: 22492192
references.citation: DNA Res. 2013 Feb;20(1):93-108
references.pmid: 23297299
references.citation: Genome Biol. 2009;10(10):R103
references.pmid: 19796385
references.citation: Genome Res. 2008 Sep;18(9):1509-17
references.pmid: 18550803
references.citation: BMC Genomics. 2013 Mar 12;14:167
references.pmid: 23496952
references.citation: Bioinformatics. 2012 Jan 1;28(1):63-8
references.pmid: 22072384
references.citation: Nat Methods. 2008 Jul;5(7):621-8
references.pmid: 18516045
references.citation: Genome Res. 2002 Apr;12(4):656-64
references.pmid: 11932250
references.citation: Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1513-8
references.pmid: 21187386
references.citation: PLoS One. 2012;7(9):e45524
references.pmid: 23049809
references.citation: Bioinformatics. 2004 Sep 1;20(13):2067-74
references.pmid: 15059830
references.citation: J Comput Biol. 2009 Aug;16(8):1117-40
references.pmid: 19689216
references.citation: Nat Protoc. 2013 Aug;8(8):1494-512
references.pmid: 23845962
references.citation: Genome Biol. 2010;11(11):R116
references.pmid: 21114842
references.citation: Genomics. 2010 Jun;95(6):315-27
references.pmid: 20211242
references.citation: Nucleic Acids Res. 2012 Nov 1;40(20):10073-83
references.pmid: 22962361
references.citation: Nat Methods. 2013 Jan;10(1):71-3
references.pmid: 23160280
references.citation: BMC Bioinformatics. 2011 Aug 25;12:354
references.pmid: 21867511
references.citation: Science. 2013 Mar 15;339(6125):1312-6
references.pmid: 23493712