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De Novo Assembly Methods for Next Generation Sequencing Data
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作者 Yiming He Zhen Zhang +2 位作者 Xiaoqing Peng Fangxiang Wu Jianxin Wang 《Tsinghua Science and Technology》 SCIE EI CAS 2013年第5期500-514,共15页
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 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. 展开更多
关键词 next-generation sequencing genome assembly overlap/lapout/consensus de bruijn graph
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