Software

I have also developed several tools to support genomic epidemiology and microbial genomics research.

For more details and to explore the code, visit my Github profile!

R packages

PhyloAMR

An R package that provides tools for phylogenetically informed analysis of antibiotic resistance and other genome-associated traits, integrating evolutionary context into genomic analyses such as genotype-phenotype relationships and lineage tracking. Repository

GeneScreener

Pipeline designed to automates running BLAST searches across many genomes, making gene identification accessible and reproducible. Repository

Command line tools

ISScreener

Workflow designed to detect insertion sequences (IS elements) from Illumina whole-genome sequencing data, helping characterize mobile genetic elements. Repository

CoverageStats

Pipeline that calculates coverage statistics for short-read sequencing data by mapped to reference sequences. Useful for quality control and comparative analyses. Repository

Phylokit

A Snakemake pipeline to generate phylogenies from sequence alignments, streamlining evolutionary analysis workflows. Repository

Fastools

A growing collection of handy scripts for manipulating FASTA files, simplifying common sequence processing tasks. Repository