Journal
GENOME BIOLOGY
Volume 17, Issue -, Pages -Publisher
BIOMED CENTRAL LTD
DOI: 10.1186/s13059-016-1074-1
Keywords
RNA-seq; Transcriptome assembly; Alternative splicing; Splicing graph; Isoform
Funding
- National Natural Science Foundation of China [61432010, 61272016, 31571354]
- USA National Science Foundation [DBI-1262107, IIS-1646333]
- Direct For Biological Sciences
- Div Of Biological Infrastructure [1262107] Funding Source: National Science Foundation
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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/.
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