General Information
| Description | A workflow management system for de novo genome assembly |
| Homepage | http://rampart.readthedocs.org/en/latest |
Publications
RAMPART: a workflow management system for de novo genome assembly
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, such as clusters and shared memory systems, where available.
Availability and implementation:
RAMPART is available under the GPLv3 license at: https://github.com/TGAC/RAMPART .
Contact:
daniel.mapleson@tgac.ac.uk
Supplementary information:
Supplementary data are available at Bioinformatics online. In addition, the user manual is available online at: http://rampart.readthedocs.org/en/latest .
Related Tools
BreakFusion
Published May 2012
Targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data
EBARDenovo
Published March 2013
Highly accurate de novo assembly of RNA-Seq with efficient chimera-detection
KAT
Published November 2016
A K-mer analysis toolkit to quality control NGS datasets and genome assemblies
FAIR Evaluation
Sorry, you must be signed in to evaluate this object.
