SIMBA

SIMBA manages bacterial genome assembly projects by integrating de novo assembly, assembly quality assessment, scaffolding and gap closure, and data quality/format conversion for NGS data.

Key Features:

• Centralized Management: Administrative control to oversee multiple bacterial genome assembly projects.
• Projects Module: Provides project overviews, performs data quality analysis, and executes data format conversions.
• Assemblies Module: Performs de novo assemblies using Mira, Minia, Newbler, and SPAdes and evaluates assembly quality with QUAST.
• Curation Module: Supports finishing operations including scaffolding contigs and closing gaps.
• Case Study Validation: Demonstrated on bacterial assemblies sequenced with the Ion Torrent Personal Genome Machine (PGM).

Scientific Applications:

• Bacterial genome assembly and finishing: Supports de novo assembly, scaffolding and gap closure for prokaryotic genomes sequenced with NGS technologies.
• Assembly quality assessment and comparison: Enables evaluation and comparison of assemblies using QUAST and multiple assemblers (Mira, Minia, Newbler, SPAdes).
• Project-level management across NGS platforms: Organizes and manages multiple sequencing projects and data formats, including datasets from Ion Torrent PGM.

Methodology:

Performs data quality analysis and data format conversions; conducts de novo assembly with Mira, Minia, Newbler and SPAdes; validates assemblies with QUAST; and applies scaffolding and gap-closure methods for finishing.