BigBacter is a pipeline aimed at simplifying bacterial genomic surveillance. At the Washington State Department of Health, we use BigBacter to support molecular epidemiological analysis and reporting for multidrug resistant organisms, Corynebacterium diptheriae, legionella, and others.
Main features
- Optimizes core genome size and phylogenetic resolution by pre-clustering samples into genetically similar sets prior to SNP calling and phylogenetic analysis.
- Saves your samples to an agency-specific database (can be stored locally or on the cloud) to keep a running database of samples and outbreaks.
- Includes stored samples from the database in analyses when they are closely related to new samples, enabling easy analysis of growing clusters.
- Multiple species/subtypes can be included in a single run.
- Optimized for speed and resource usage.
- Generates report-ready figures.
Main analyses
- Recombination-aware core SNP analysis (Snippy and Gubbins)
- Accessory distance analysis (PopPUNK)
- Phylogenetic analysis (IQTREE2 or Rapidnj)
Main outputs
- Phylogenetic trees (Core SNPs)
- Distance matrices (Accessory distance and Core SNPs)
- Tabulated summary (QC metrics, linkage summaries, and more!)
- Outputs are summarized in Microreact files