Below are the main software packages developed in the lab. Most of them live in the
lab's GitHub organization,
where you can also find the analysis code for most of our publications.
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microGWAS
A computational pipeline to perform large-scale bacterial genome-wide association studies, from genome assemblies to annotated hits.
Repository
· Documentation
· Burgaya, Damaris, Fiebig et al., Microbial Genomics, 2025
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pyseer
Sequence element enrichment analysis for microbial pangenome-wide association studies, reimplemented in python.
Repository
· Documentation
· Lees, Galardini et al., Bioinformatics, 2018
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panfeed
A k-mer counter that streams gene-cluster specific k-mers while keeping positional information, for more interpretable bacterial GWAS.
Repository
· Sommer, Djamalova et al., Microbial Genomics, 2023
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tenet
Transmission Events NETworks: a pipeline to go from bacterial genome assemblies to transmission events networks.
Repository
· Burgaya et al., medRxiv preprint, 2026
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SARS-CoV-2 epistasis
Estimation of epistatic interactions from large SARS-CoV-2 genome collections, using mutual information.
Repository
· Innocenti et al., Genome Biology, 2024
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plate_reader_evolution
Tools to run and analyse evolution experiments in microplate formats: parsing plate reader data, computing growth rates and MICs, plotting, and Opentrons robot protocols.
Repository