Title of article :
De Novo Assembly Methods for Next Generation Sequencing Data
Author/Authors :
He, Yiming Central South University - School of Information Science and Engineering, China , Zhang, Zhen Central South University - School of Information Science and Engineering, China , Peng, Xiaoqing Central South University - School of Information Science and Engineering, China , Peng, Xiaoqing Morehouse School of Medicine, USA , Wu, Fangxiang University of Saskatchewan - Department of Mechanical Engineering and Division of Biomedical Engineering, Canada , Wang, Jianxin Central South University - School of Information Science and Engineering, China
Abstract :
The recent breakthroughs in next-generation sequencing technologies, such as those of Roche 454,Illumina/Solexa, and ABI SOLID, have dramatically reduced the cost of producing short reads of the genome of new species. The huge volume of reads, along with short read length, high coverage, and sequencing errors, poses a great challenge to de novo genome assembly. However, the paired-end information provides a new solution to these problems. In this paper, we review and compare some current assembly tools, including Newbler, CAP3, Velvet, SOAPdenovo, AllPaths, Abyss, IDBA, PE-Assembly, and Telescoper. In general, we compare the seed extension and graph-based methods that use the overlap/lapout/consensus approach and the de Bruijn graph approach for assembly. At the end of the paper, we summarize these methods and discuss the future directions of genome assembly.
Keywords :
next , generation sequencing , genome assembly , overlap , lapout , consensus , de Bruijn graph
Journal title :
Tsinghua Science and Technology
Journal title :
Tsinghua Science and Technology
