An Effective Approach for Assembling Very Short Reads from Next Generation Sequencer

概要

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de novo DNA sequence assembly is very important in genome sequence analysis. In this paper, we deeply investigated two of the major approaches for de novo DNA sequence assembly of very short reads: overlap-layout-consensus (OLC) and Eulerian path using a de Bruijn graph. We proposed a new assembling technique by combining OLC and Eulerian path in hierarchical process. The contigs yielded by these two approaches are treated as reads and are assembled again to yield longer contigs than the previous contigs. We tested the combined approach by using three Illumina very-short-read datasets and four error-free reads simulated datasets. As results, the combined approach yielded longer contigs, in term of N50 and maximum contigs, than OLC or Eulerian path approach alone.
2011-03-03