RAMPART: a workflow management system for de novo genome assembly.

ABSTRACT:

Motivation

The de novo assembly of genomes from whole- genome shotgun sequence data is a computationally intensive, multi-stage task and it is not known a priori which methods and parameter settings will produce optimal results. In current de novo assembly projects, a popular strategy involves trying many approaches, using different tools and settings, and then comparing and contrasting the results in order to select a final assembly for publication.

Results

Herein, we present RAMPART, a configurable workflow management system for de novo genome assembly, which helps the user identify combinations of third-party tools and settings that provide good results for their particular genome and sequenced reads. RAMPART is designed to exploit High performance computing environments,

SUBMITTER: Mapleson D 

PROVIDER: S-EPMC4443680 | biostudies-literature | 2015 Jun

REPOSITORIES: biostudies-literature