SLR: a scaffolding algorithm based on long reads and contig classification.

ABSTRACT:

Background

Scaffolding is an important step in genome assembly that orders and orients the contigs produced by assemblers. However, repetitive regions in contigs usually prevent scaffolding from producing accurate results. How to solve the problem of repetitive regions has received a great deal of attention. In the past few years, long reads sequenced by third-generation sequencing technologies (Pacific Biosciences and Oxford Nanopore) have been demonstrated to be useful for sequencing repetitive regions in genomes. Although some stand-alone scaffolding algorithms based on long reads have been presented, scaffolding still requires a new strategy to take full advantage of the characteristics of long reads.

Results

Here, we present a new scaffolding algorithm based on long rea

SUBMITTER: Luo J 

PROVIDER: S-EPMC6820941 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature