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PoODLE (Phylogenomic Overview for Detection of Linkages for Epidemiologists) is a bioinformatics pipeline for identifying genomic relatedness between bacterial isolates. Starting from a samplesheet containing sequencing reads (FASTQ), genome assemblies (FASTA), and annotation files (GFF/GBK), PoODLE performs variant calling, recombination filtering, phylogenetic reconstruction, pangenome analysis and Mash distance estimation. The pipeline produces linkage tables and an interactive HTML report for each cluster with trees, pangenome profiles, and distance matrices.
Genomes analyzed with sequencing pipelines (e.g.,PHoeNIx, Bactopia, TheiaProk, custom workflows) or obtained from public repositories (e.g., AllTheBacteria, NCBI) can be analyzed with CorGe+ or with other clustering pipelines to identify preliminary genetic groupings and prioritize related samples.
These grouped isolates can then be analyzed with PoODLE which enables detailed within-group investigation through SNP-based approaches and pangenome analysis, supporting fine-scale discrimination of closely related isolates. This workflow provides the resolution needed for routine surveillance, cluster validation, and outbreak investigation.
- Processes multiple species and clusters in parallel
- Optimized to reuse previous variant calling results (useful in routine surveillance, where clusters grow incrementally)
- Generates HTML reports and linkage tables to facilitate interpretations
High-level steps:
- Reference-based variant calling with
Snippy - Recombination filtering with
Gubbins(optional) - Constant site calculation from genome alignment with
snp-sites - Phylogeny with
IQ-TREE - Pairwise SNP distance calculation with
snp-dists - Linkage analysis based on pairwise SNP distances
- Pangenome analysis with
Panaroo - Whole-genome distance tree with
MashTree(optional) - Report generation including trees, distance matrices, and pangenome plots