title: BinPacker: Packing-Based De Novo Transcriptome Assembly from RNA-seq Data.
abstract: High-throughput RNA-seq technology has provided an unprecedented opportunity to reveal the very complex structures of transcriptomes. However, it is an important and highly challenging task to assemble vast amounts of short RNA-seq reads into transcriptomes with alternative splicing isoforms. In this study, we present a novel de novo assembler, BinPacker, by modeling the transcriptome assembly problem as tracking a set of trajectories of items with their sizes representing coverage of their corresponding isoforms by solving a series of bin-packing problems. This approach, which subtly integrates coverage information into the procedure, has two exclusive features: 1) only splicing junctions are involved in the assembling procedure; 2) massive pell-mell reads are assembled seemingly by moving a comb along junction edges on a splicing graph. Being tested on both real and simulated RNA-seq datasets, it outperforms almost all the existing de novo assemblers on all the tested datasets, and even outperforms those ab initio assemblers on the real dog dataset. In addition, it runs substantially faster and requires less memory space than most of the assemblers. BinPacker is published under GNU GENERAL PUBLIC LICENSE and the source is available from: http://sourceforge.net/projects/transcriptomeassembly/files/BinPacker_1.0.tar.gz/download. Quick installation version is available from: http://sourceforge.net/projects/transcriptomeassembly/files/BinPacker_binary.tar.gz/download.
authors.affiliation: School of Mathematics, Shandong University, Jinan, China.
authors.forename: Juntao
authors.initials: J
authors.lastname: Liu
authors.affiliation: School of Mathematics, Shandong University, Jinan, China.
authors.forename: Guojun
authors.initials: G
authors.lastname: Li
authors.affiliation: School of Mathematics, Shandong University, Jinan, China.
authors.forename: Zheng
authors.initials: Z
authors.lastname: Chang
authors.affiliation: School of Mathematics, Shandong University, Jinan, China.
authors.forename: Ting
authors.initials: T
authors.lastname: Yu
authors.affiliation: School of Mathematics, Shandong University, Jinan, China.
authors.forename: Bingqiang
authors.initials: B
authors.lastname: Liu
authors.affiliation: High Performance Computing Center, University of Arkansas, Fayetteville, Arkansas, United States of America.
authors.forename: Rick
authors.initials: R
authors.lastname: McMullen
authors.affiliation: Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America.
authors.forename: Pengyin
authors.initials: P
authors.lastname: Chen
authors.affiliation: Department of Computer Science, Arkansas State University, Jonesboro, Arkansas, United States of America.
authors.forename: Xiuzhen
authors.initials: X
authors.lastname: Huang
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology; D004285:Dogs; D020869:Gene Expression Profiling / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D051379:Mice; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D059467:Transcriptome / Q000235:genetics*
chemical_list: D012333:RNA, Messenger