Staphopia

Staphopia analyzes Staphylococcus aureus whole-genome sequencing data to perform assembly, variant calling, gene annotation, and population-scale genomic analyses.

Key Features:

• Analysis Pipeline: Implemented in Python with submodules that use open-source bioinformatics tools to process raw FASTQ reads through quality control, error correction, and coverage normalization to approximately 100x per chromosome.
• Genomic Analysis: Performs both de novo assembly-based and mapping-based analyses with automated gene calling and annotation on assembled contigs and read-mapping to identify SNPs and indels using the Staphylococcus aureus Type strain N315 chromosome as reference.
• Database and API: Maintains a comprehensive database of S. aureus genomic data accessible via an Application Programming Interface (API).
• Large-scale Public Data Processing: Processes tens of thousands of public whole-genome shotgun projects from EBI's ENA, including analysis of over 43,000 S. aureus genome projects (November 2017).

Scientific Applications:

• Genotype, Antibiotic Resistance, and Virulence Profiling: Provides genotype assignments and profiles of antibiotic resistance and virulence genes specific to S. aureus.
• Diversity and Epidemiology Studies: Enables population-level analyses that revealed multi-locus sequence type distributions (the top ten STs account for 70% of genomes) and MRSA prevalence (64%) across >43,000 genomes (November 2017).
• Non-redundant Diversity Set: Curated a non-redundant diversity set of 380 high-quality genomes, each representing different sequence types, for studies of S. aureus evolution and diversity.

Methodology:

Implemented in Python with submodules using open-source bioinformatics tools; accepts raw FASTQ reads that undergo quality control filtration, error correction, and down-sampling to ~100x per chromosome; performs de novo assembly and mapping-based analyses; conducts automated gene calling and annotation on assembled contigs; and uses read-mapping to identify SNPs and indels against the S. aureus Type strain N315 reference.