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StringTie enables improved reconstruction of a transcriptome from RNA-seq reads.

Abstract：

:Methods used to sequence the transcriptome often produce more than 200 million short sequences. We introduce StringTie, a computational method that applies a network flow algorithm originally developed in optimization theory, together with optional de novo assembly, to assemble these complex data sets into transcripts. When used to analyze both simulated and real data sets, StringTie produces more complete and accurate reconstructions of genes and better estimates of expression levels, compared with other leading transcript assembly programs including Cufflinks, IsoLasso, Scripture and Traph. For example, on 90 million reads from human blood, StringTie correctly assembled 10,990 transcripts, whereas the next best assembly was of 7,187 transcripts by Cufflinks, which is a 53% increase in transcripts assembled. On a simulated data set, StringTie correctly assembled 7,559 transcripts, which is 20% more than the 6,310 assembled by Cufflinks. As well as producing a more complete transcriptome assembly, StringTie runs faster on all data sets tested to date compared with other assembly software, including Cufflinks.

journal_name

Nat Biotechnol

journal_title

Nature biotechnology

authors

Pertea M,Pertea GM,Antonescu CM,Chang TC,Mendell JT,Salzberg SL

doi

10.1038/nbt.3122

subject

Has Abstract

pub_date

2015-03-01 00:00:00

pages

290-5

issue

3

eissn

1087-0156

issn

1546-1696

pii

nbt.3122

journal_volume

33

pub_type

杂志文章

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