De novo genome assembly for third generation sequencing data

摘要

The second generation sequencing techniques opened doors to further research on a world scale, because the cost of DNA sequencing dropped significantly. However, the second generation sequencing technology has some drawbacks, mainly short read length. In 2017 the new devices, that use realtime sequencing started to be available. This apporach, called "the third-generation sequencing" achieve read length of 20kbp and error rate about 15%. As a consequence of this process new DNA assemblers were developed. In this article we propose an implementation of Overlap Graph-based de novo assembly algorithm for third-generation sequencing data. The proposed method involves graph algorithms and dynamic programming, optimized using a MinHash filter. The solution has been tested on both simulated and real data of bacteria obtained from Oxford Nanopore MinlON sequencer. The algorithm is included in "OLC" module of the dnaasm de novo assembler, cation provides command line interface as well as web browser-based client.