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1. pf-survey pf-survey Public

   Surveillance for bacterial genomes from paired-end short reads; quality control, assembly, annotation, multi-locus sequence typing; for isolates 🛰️

2. pf-lineage pf-lineage Public

   Lineage-focused molecular typing and comparative phylogenomics; de-clustering, alignment, variant calling, phylogenetics; for isolate sets 🔭

3. pathfinder pathfinder Public

   Python package to manage pipelines and data processing; command line interface 🐍

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4. datasets datasets Public

   Pathfinder community datasets and templating: distribution of local analyses 🐁

5. database database Public

   Python package for database models 🐍 and access point interface for MongoDB 🌱

6. app app Public

   Vue app for database interface and pipeline data visualizations 🌻