RESEARCH ARTICLE

A Short Sequence Splicing Method for Genome Assembly Using a Three-Dimensional Mixing-Pool of BAC Clones and High-throughput Technology

The Open Biotechnology Journal 27 Oct 2015 RESEARCH ARTICLE DOI: 10.2174/1874070701509010210

Abstract

Current genome sequencing techniques are expensive, and it is still a major challenge to obtain an individual whole-genome sequence. To reduce the cost of sequencing, this paper introduced a high-throughput sequencing strategy using a three-dimensional mixing-pools based on the cube. Following the strategy, BAC clones were injected into each vertex of the cube, and sequencing of each plane provided information about multiple clones, thereby significantly reducing the cost of sequencing. In addition, Velvet was used to assemble the sequencing data. The scaffold generated from Velvet contained a number of contigs, which were orderless. Therefore, to address this problem, a scaffold assembly algorithm based on multi-way trees was used. The algorithm used a multi-way tree to build the framework of chromosomes, and subsequently, the frame was filled to complete the scaffold assembly. This algorithm alone outperformed Velvet in the assembling of a scaffold.

Keywords: BAC clone data, scaffold assembly algorithm, three-dimensional mixing-pool.
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