LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly.

ABSTRACT:

Background

Completing a genome is an important goal of genome assembly. However, many assemblies, including reference assemblies, are unfinished and have a number of gaps. Long reads obtained from third-generation sequencing (TGS) platforms can help close these gaps and improve assembly contiguity. However, current gap-closure approaches using long reads require extensive runtime and high memory usage. Thus, a fast and memory-efficient approach using long reads is needed to obtain complete genomes.

Findings

We developed LR_Gapcloser to rapidly and efficiently close the gaps in genome assembly. This tool utilizes long reads generated from TGS sequencing platforms. Tested on de novo assembled gaps, repeat-derived gaps, and real gaps, LR_Gapcloser closed a higher number of gaps

SUBMITTER: Xu GC 

PROVIDER: S-EPMC6324547 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature