rampart

RAMPART: Configurable framework for de novo genome assembly evaluation

RAMPART orchestrates and evaluates multiple third-party de novo genome assembly tools and parameter configurations to identify optimal assembly strategies for specific genomes and sequencing reads.

Key Features:

• Configurability: Enables systematic exploration of diverse combinations of third-party assemblers and parameter settings tailored to specific genomes and sequenced reads.
• Workflow Management: Executes and compares multiple assembly approaches concurrently, automating performance assessment across tools and configurations.
• High-Performance Computing Integration: Optimized for clusters and shared memory systems to support scalable, large-scale genome assembly analyses.

Scientific Applications:

• De Novo Genome Assembly: Supports generation and evaluation of reference-free genome assemblies for downstream gene annotation, comparative genomics, and evolutionary analysis.

Methodology:

RAMPART implements a systematic de novo assembly benchmarking workflow in which multiple third-party assemblers and parameter sets are configured, executed in parallel on high-performance computing systems, and quantitatively compared using assembly quality metrics to select optimal assemblies for specific genomic datasets.