GAAP: Genome-organization-framework-Assisted Assembly Pipeline for prokaryotic genomes.

ABSTRACT:

Background

Next-generation sequencing (NGS) technologies have greatly promoted the genomic study of prokaryotes. However, highly fragmented assemblies due to short reads from NGS are still a limiting factor in gaining insights into the genome biology. Reference-assisted tools are promising in genome assembly, but tend to result in false assembly when the assigned reference has extensive rearrangements.

Results

Herein, we present GAAP, a genome assembly pipeline for scaffolding based on core-gene-defined Genome Organizational Framework (cGOF) described in our previous study. Instead of assigning references, we use the multiple-reference-derived cGOFs as indexes to assist in order and orientation of the scaffolds and build a skeleton structure, and then use read pairs to exten

SUBMITTER: Yuan L 

PROVIDER: S-EPMC5310280 | biostudies-literature | 2017 Jan

REPOSITORIES: biostudies-literature