Open-Source Software 🧬¶
Bioinformatics command-line tools, genomic surveillance pipelines, and high-performance Python and Rust libraries that I have built or lead as part of my research in bacterial genomics and antimicrobial resistance.
Explore individual project pages below, including Kaptive 3, SideroScanner, pyfgs, bart, rammappy, and eris, or browse related peer-reviewed articles on the Publications page.
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Kaptive 3 Python
Fast and accurate in silico serotyping and surface polysaccharide locus typing for bacterial genomes.
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SideroScanner Python
A bioinformatics tool for identifying and annotating iron-regulated outer membrane proteins (IROMPs) in bacterial genomes.
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pyfgs Rust / Python
Python bindings to FragGeneScanRs for fast, error-tolerant bacterial open reading frame (ORF) prediction.
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bart Rust / Python
Bacterial Read Typer — fast targeted locus typing directly from raw sequencing reads.
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rammappy Rust / Python
A Python interface to rammap, providing native Rust-powered minimap2 alignments in Python.
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eris Python
Graph-aware contextual annotation of targeted genomic features in bacterial assemblies.