AutoAssemblyD

AutoAssemblyD orchestrates genome assembly of next-generation sequencing short reads by integrating multiple assemblers and standardizing input parameters for assembly tasks.

Key Features:

• Multi-assembler integration: Supports assemblers and aligners including Velvet, Abyss, Euler-SR, Mira, Edna, Maq, SHRiMP, Newbler, ALLPATHS, Bowtie, and BWA.
• XML template-based configuration: Uses XML templates to specify and standardize assembler input parameters across different algorithms.
• Local and remote execution: Executes genome assemblies both locally and on remote computing resources.
• Remote submission and management: Provides capabilities for remote submission and management of assembly tasks.
• High-throughput data handling: Processes large volumes of next-generation sequencing short-read data for de novo and reference-based assembly workflows.

Scientific Applications:

• Genome assembly from NGS reads: Produces assembled genomes from high-throughput short-read sequencing datasets.
• Comparative genomics and evolutionary biology: Enables generation of assemblies used in comparative and evolutionary analyses.
• Applied genomics and personalized medicine: Supports assembly generation for projects in genomics and personalized medicine where assembled genomes are required.
• Assembly strategy optimization: Facilitates comparison of results across multiple assemblers to optimize assembly strategies for specific datasets.

Methodology:

Implements a unified platform that integrates multiple assemblers, standardizes input parameters via XML templates, and supports local and remote submission and management of assembly tasks.