title: TransComb: genome-guided transcriptome assembly via combing junctions in splicing graphs.
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/ .
authors.affiliation: School of Mathematics, Shandong University, Jinan, 250100, China.|Department of Computer Science and Engineering, University of California, Riverside, CA, 92521, USA.
authors.forename: Juntao
authors.initials: J
authors.lastname: Liu
authors.affiliation: School of Mathematics, Shandong University, Jinan, 250100, China.
authors.forename: Ting
authors.initials: T
authors.lastname: Yu
authors.affiliation: Department of Computer Science and Engineering, University of California, Riverside, CA, 92521, USA. jiang@cs.ucr.edu.|MOE Key Lab of Bioinformatics and Bioinformatics Division, TNLIST/Department of Computer Science and Technology, Tsinghua University, Beijing, China. jiang@cs.ucr.edu.|Institute of Integrative of Genome Biology, University of California, Riverside, CA, 92521, USA. jiang@cs.ucr.edu.
authors.forename: Tao
authors.initials: T
authors.lastname: Jiang
authors.affiliation: School of Mathematics, Shandong University, Jinan, 250100, China. guojunsdu@gmail.com.
authors.forename: Guojun
authors.initials: G
authors.lastname: Li
mesh_terms: D000465:Algorithms; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D006801:Humans; D012313:RNA / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D059467:Transcriptome / Q000235:genetics*
chemical_list: D012313:RNA
keywords: Alternative splicing; Isoform; RNA-seq; Splicing graph; Transcriptome assembly