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 movin

SUBMITTER: Liu J 

PROVIDER: S-EPMC4760927 | biostudies-literature | 2016 Feb

REPOSITORIES: biostudies-literature