Genome Assembly Algorithms for Second- and Third-Generation Sequencing

Abstract

The 2nd and 3rd generation sequencing technologies have been widely used on the de novo sequencing and assembly of many genomes in the biosphere. However, the assembly of large and complex genomes is often fragmented, and the assembly speed and accuracy are still unsatisfactory. In this talk, we first highlight the challenges of repeats and sequencing bias of 2nd generation sequencing. A novel assembler is developed for overcoming these challenges by integrating the string and de Bruijn graphs. In the second part of the talk, we presented a hybrid assembler for 2nd and 3rd generation sequencing, which used FM-index for both error correction and inexact overlap computation. The hybrid approach is able to assemble higher-quality genomes (N50 > 1Mb) under lower-coverage (15x) 3rd generation sequencing in comparison with other methods.