Conversion of Mate-Pair Reads into Long Sequences for Improving Assembly Scaffolding

Abstract

Mate-pair sequencing is a technology for sequencing two ends of long DNA fragments, which has been widely used in genome scaffolding. Although the cost of mate-pair sequencing is now affordable, its accuracy has been limited by the lower quality and contamination. The 3rd generation sequencing is able to generate long reads for genome scaffolding. However, the error rates and cost are still too high. This paper aims to convert low-cost mate-pair reads into long reads using computational approaches, which has the benefits of both mate-pair reads and long reads for scaffolding. We test our methods by using several real datasets and validate the accuracy of converted long reads. In addition, the scaffolding results are compared using mate-pair reads, long reads, and mixture of both material.