SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• Next-Generation Sequencing (NGS) has enabled large-scale genome projects, particularly in prokaryotes.
• Diverse NGS platforms necessitate distinct assembly strategies and software, demanding significant user expertise.
• These complexities often impede the timely completion of bacterial genome assembly projects.

Purpose of the Study:

• To develop a user-friendly web tool, SIMBA (Simple Manager for Bacterial Assemblies), to simplify bacterial genome assembly and finishing.
• To provide a centralized management system for genome sequencing projects, accessible to bioinformaticians with varying computational skills.

Main Methods:

• SIMBA integrates multiple de novo assembly tools (Mira, Minia, Newbler, SPAdes) and quality validation software (QUAST).
• The workflow includes modules for project overview, data quality analysis, format conversion, assembly, and curation (scaffolding, gap closure).
• A case study using Ion Torrent PGM data validated SIMBA's efficacy in managing bacterial assembly projects.

Main Results:

• SIMBA offers an intuitive interface for executing complex assembly processes.
• The tool effectively manages genome sequencing projects, from data preparation to final assembly and finishing.
• Validation confirmed SIMBA's capability to handle bacterial assemblies from Ion Torrent PGM sequencing.

Conclusions:

• SIMBA functions as a comprehensive project management system for bacterial genome assemblies.
• It is valuable for managing multiple genome projects within research laboratories.
• The source code is publicly available for local installation.