title: Augmenting transcriptome assembly by combining de novo and genome-guided tools.
abstract: Researchers interested in studying and constructing transcriptomes, especially for non-model species, face the conundrum of choosing from a number of available de novo and genome-guided assemblers. None of the popular assembly tools in use today achieve requisite sensitivity, specificity or recovery of full-length transcripts on their own. Here, we present a comprehensive comparative study of the performance of various assemblers. Additionally, we present an approach to combinatorially augment transciptome assembly by using both de novo and genome-guided tools. In our study, we obtained the best recovery and most full-length transcripts with Trinity and TopHat1-Cufflinks, respectively. The sensitivity of the assembly and isoform recovery was superior, without compromising much on the specificity, when transcripts from Trinity were augmented with those from TopHat1-Cufflinks.
authors.affiliation: Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, India.
authors.forename: Prachi
authors.initials: P
authors.lastname: Jain
authors.affiliation: Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, India.
authors.forename: Neeraja M
authors.initials: NM
authors.lastname: Krishnan
authors.affiliation: Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, India.|Strand Life Sciences, Hebbal, Bangalore, India.
authors.forename: Binay
authors.initials: B
authors.lastname: Panda
keywords: De novo transcriptome assembly; Genome-guided transcriptome assembly; Misassembly; Model assembly; Transcriptome; Transcriptome assembly
references.citation: Nat Rev Genet. 2013 Mar;14(3):157-67
references.pmid: 23358380
references.citation: Nat Biotechnol. 2010 May;28(5):511-5
references.pmid: 20436464
references.citation: PLoS One. 2012;7(2):e31410
references.pmid: 22384018
references.citation: Bioinformatics. 2011 Sep 1;27(17):2325-9
references.pmid: 21697122
references.citation: Nat Protoc. 2012 Mar 01;7(3):562-78
references.pmid: 22383036
references.citation: Bioinformatics. 2009 Nov 1;25(21):2872-7
references.pmid: 19528083
references.citation: Nat Genet. 1996 Dec;14(4):457-60
references.pmid: 8944026
references.citation: Bioinformatics. 2010 Apr 1;26(7):873-81
references.pmid: 20147302
references.citation: Proc Natl Acad Sci U S A. 1996 Oct 1;93(20):10614-9
references.pmid: 8855227
references.citation: Nat Biotechnol. 2012 Nov;30(11):1084-94
references.pmid: 23138308
references.citation: Science. 1999 Oct 15;286(5439):531-7
references.pmid: 10521349
references.citation: Nat Protoc. 2013 Aug;8(8):1494-512
references.pmid: 23845962
references.citation: Bioinformatics. 2010 Mar 15;26(6):841-2
references.pmid: 20110278
references.citation: Nat Methods. 2010 Nov;7(11):909-12
references.pmid: 20935650
references.citation: PLoS Comput Biol. 2008 Sep 26;4(9):e1000186
references.pmid: 18818729
references.citation: Annu Rev Plant Biol. 2009;60:305-33
references.pmid: 19575585
references.citation: Curr Protoc Bioinformatics. 2010 Dec;Chapter 11:Unit 11.7
references.pmid: 21154709
references.citation: BMC Genomics. 2012 Mar 14;13:92
references.pmid: 22417298
references.citation: Nat Biotechnol. 2011 May 15;29(7):644-52
references.pmid: 21572440
references.citation: Genome Res. 2010 Sep;20(9):1165-73
references.pmid: 20508146
references.citation: Science. 1995 Oct 20;270(5235):467-70
references.pmid: 7569999
references.citation: Mol Biol Evol. 2009 Dec;26(12):2731-44
references.pmid: 19706727
references.citation: Genome Res. 2008 May;18(5):821-9
references.pmid: 18349386
references.citation: Nat Rev Genet. 2009 Jan;10(1):57-63
references.pmid: 19015660
references.citation: Genome Res. 2010 Feb;20(2):265-72
references.pmid: 20019144
references.citation: Bioinformatics. 2009 May 1;25(9):1105-11
references.pmid: 19289445
references.citation: Bioinformatics. 2012 Apr 15;28(8):1086-92
references.pmid: 22368243
references.citation: Nat Rev Genet. 2011 Feb;12(2):87-98
references.pmid: 21191423
references.citation: Nat Methods. 2008 Jul;5(7):621-8
references.pmid: 18516045
references.citation: Science. 2007 Oct 19;318(5849):441-4
references.pmid: 17901299
references.citation: Trends Biotechnol. 2002 Aug;20(8):315-6
references.pmid: 12127268
references.citation: Methods Mol Biol. 2011;759:125-32
references.pmid: 21863485
references.citation: Genome Res. 2004 Jul;14(7):1394-403
references.pmid: 15231754
references.citation: Genome Biol. 2013 Apr 25;14(4):R36
references.pmid: 23618408
references.citation: Curr Opin Chem Biol. 2011 Aug;15(4):505-15
references.pmid: 21684801
references.citation: Nat Rev Genet. 2011 Sep 07;12(10):671-82
references.pmid: 21897427
references.citation: Genome Res. 2009 Jun;19(6):1117-23
references.pmid: 19251739
references.citation: Genome Inform. 2008;21:3-14
references.pmid: 19425143
references.citation: Am J Bot. 2012 Feb;99(2):175-85
references.pmid: 22312116
references.citation: Nucleic Acids Res. 2012 Nov 1;40(20):10073-83
references.pmid: 22962361
references.citation: Bioinformatics. 2014 Jun 15;30(12):1660-6
references.pmid: 24532719
references.citation: J Mol Biol. 1990 Oct 5;215(3):403-10
references.pmid: 2231712
references.citation: Int J Dev Biol. 2009;53(5-6):765-73
references.pmid: 19557682