title: DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies.
abstract: The highly anticipated transition from next generation sequencing (NGS) to third generation sequencing (3GS) has been difficult primarily due to high error rates and excessive sequencing cost. The high error rates make the assembly of long erroneous reads of large genomes challenging because existing software solutions are often overwhelmed by error correction tasks. Here we report a hybrid assembly approach that simultaneously utilizes NGS and 3GS data to address both issues. We gain advantages from three general and basic design principles: (i) Compact representation of the long reads leads to efficient alignments. (ii) Base-level errors can be skipped; structural errors need to be detected and corrected. (iii) Structurally correct 3GS reads are assembled and polished. In our implementation, preassembled NGS contigs are used to derive the compact representation of the long reads, motivating an algorithmic conversion from a de Bruijn graph to an overlap graph, the two major assembly paradigms. Moreover, since NGS and 3GS data can compensate for each other, our hybrid assembly approach reduces both of their sequencing requirements. Experiments show that our software is able to assemble mammalian-sized genomes orders of magnitude more quickly than existing methods without consuming a lot of memory, while saving about half of the sequencing cost.
authors: Department of Computer Science, Institute for Advanced Computer Studies, University of Maryland, College Park, MD 20742, USA.|Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 China.
authors: Chengxi
authors: C
authors: Ye
authors: Department of Computer Science, Institute for Advanced Computer Studies, University of Maryland, College Park, MD 20742, USA.
authors: Christopher M
authors: CM
authors: Hill
authors: Agricultural Genome Institute, Chinese Academy of Agricultural Sciences, No.7 Pengfei Road, Dapeng New District, Shenzhen, Guangdong 518120, China.
authors: Shigang
authors: S
authors: Wu
authors: Agricultural Genome Institute, Chinese Academy of Agricultural Sciences, No.7 Pengfei Road, Dapeng New District, Shenzhen, Guangdong 518120, China.
authors: Jue
authors: J
authors: Ruan
authors: Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 China.
authors: Zhanshan Sam
authors: ZS
authors: Ma
mesh_terms: D019295:Computational Biology / Q000379:methods*; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*