title: Full-length transcriptome assembly from RNA-Seq data without a reference genome.
abstract: Massively parallel sequencing of cDNA has enabled deep and efficient probing of transcriptomes. Current approaches for transcript reconstruction from such data often rely on aligning reads to a reference genome, and are thus unsuitable for samples with a partial or missing reference genome. Here we present the Trinity method for de novo assembly of full-length transcripts and evaluate it on samples from fission yeast, mouse and whitefly, whose reference genome is not yet available. By efficiently constructing and analyzing sets of de Bruijn graphs, Trinity fully reconstructs a large fraction of transcripts, including alternatively spliced isoforms and transcripts from recently duplicated genes. Compared with other de novo transcriptome assemblers, Trinity recovers more full-length transcripts across a broad range of expression levels, with a sensitivity similar to methods that rely on genome alignments. Our approach provides a unified solution for transcriptome reconstruction in any sample, especially in the absence of a reference genome.
authors.affiliation: Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA.
authors.forename: Manfred G
authors.initials: MG
authors.lastname: Grabherr
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Haas
authors.forename: Moran
authors.initials: M
authors.lastname: Yassour
authors.forename: Joshua Z
authors.initials: JZ
authors.lastname: Levin
authors.forename: Dawn A
authors.initials: DA
authors.lastname: Thompson
authors.forename: Ido
authors.initials: I
authors.lastname: Amit
authors.forename: Xian
authors.initials: X
authors.lastname: Adiconis
authors.forename: Lin
authors.initials: L
authors.lastname: Fan
authors.forename: Raktima
authors.initials: R
authors.lastname: Raychowdhury
authors.forename: Qiandong
authors.initials: Q
authors.lastname: Zeng
authors.forename: Zehua
authors.initials: Z
authors.lastname: Chen
authors.forename: Evan
authors.initials: E
authors.lastname: Mauceli
authors.forename: Nir
authors.initials: N
authors.lastname: Hacohen
authors.forename: Andreas
authors.initials: A
authors.lastname: Gnirke
authors.forename: Nicholas
authors.initials: N
authors.lastname: Rhind
authors.forename: Federica
authors.initials: F
authors.lastname: di Palma
authors.forename: Bruce W
authors.initials: BW
authors.lastname: Birren
authors.forename: Chad
authors.initials: C
authors.lastname: Nusbaum
authors.forename: Kerstin
authors.initials: K
authors.lastname: Lindblad-Toh
authors.forename: Nir
authors.initials: N
authors.lastname: Friedman
authors.forename: Aviv
authors.initials: A
authors.lastname: Regev
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D020869:Gene Expression Profiling / Q000379:methods*; D008969:Molecular Sequence Data; D012313:RNA / Q000737:chemistry* / Q000235:genetics*; D012016:Reference Values; D017423:Sequence Analysis, RNA / Q000379:methods* / Q000592:standards; D059467:Transcriptome
chemical_list: D012313:RNA