title: Evaluating de Bruijn graph assemblers on 454 transcriptomic data.
abstract: Next generation sequencing (NGS) technologies have greatly changed the landscape of transcriptomic studies of non-model organisms. Since there is no reference genome available, de novo assembly methods play key roles in the analysis of these data sets. Because of the huge amount of data generated by NGS technologies for each run, many assemblers, e.g., ABySS, Velvet and Trinity, are developed based on a de Bruijn graph due to its time- and space-efficiency. However, most of these assemblers were developed initially for the Illumina/Solexa platform. The performance of these assemblers on 454 transcriptomic data is unknown. In this study, we evaluated and compared the relative performance of these de Bruijn graph based assemblers on both simulated and real 454 transcriptomic data. The results suggest that Trinity, the Illumina/Solexa-specialized transcriptomic assembler, performs the best among the multiple de Bruijn graph assemblers, comparable to or even outperforming the standard 454 assembler Newbler which is based on the overlap-layout-consensus algorithm. Our evaluation is expected to provide helpful guidance for researchers to choose assemblers when analyzing 454 transcriptomic data.
authors.affiliation: MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
authors.forename: Xianwen
authors.initials: X
authors.lastname: Ren
authors.forename: Tao
authors.initials: T
authors.lastname: Liu
authors.forename: Jie
authors.initials: J
authors.lastname: Dong
authors.forename: Lilian
authors.initials: L
authors.lastname: Sun
authors.forename: Jian
authors.initials: J
authors.lastname: Yang
authors.forename: Yafang
authors.initials: Y
authors.lastname: Zhu
authors.forename: Qi
authors.initials: Q
authors.lastname: Jin
mesh_terms: D003198:Computer Simulation; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D008957:Models, Genetic; D012441:Saccharomyces cerevisiae / Q000235:genetics; D012680:Sensitivity and Specificity; D012984:Software; D059467:Transcriptome / Q000235:genetics*; D014249:Trichophyton / Q000235:genetics