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Genome Biology

, 17:213

First Online: 19 October 2016Received: 27 July 2016Accepted: 28 September 2016

Abstract

Transcriptome assemblers aim to reconstruct full-length transcripts from RNA-seq data. We present TransComb, a genome-guided assembler developed based on a junction graph, weighted by a bin-packing strategy and paired-end information. A newly designed extension method based on weighted junction graphs can accurately extract paths representing expressed transcripts, whether they have low or high expression levels. Tested on both simulated and real datasets, TransComb demonstrates significant improvements in both recall and precision over leading assemblers, including StringTie, Cufflinks, Bayesembler, and Traph. In addition, it runs much faster and requires less memory on average. TransComb is available at http:-sourceforge.net-projects-transcriptomeassembly-files-.

KeywordsRNA-seq Transcriptome assembly Alternative splicing Splicing graph Isoform AbbreviationsNCBINational Center for Biotechnology Information

RNA-seqRNA sequencing

SRASequence Read Archive

Electronic supplementary materialThe online version of this article doi:10.1186-s13059-016-1074-1 contains supplementary material, which is available to authorized users.

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Autor: Juntao Liu - Ting Yu - Tao Jiang - Guojun Li

Fuente: https://link.springer.com/



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