Software

I have also developed several open-source tools to support genomic epidemiology and microbial genomics research.
These tools aim to simplify common workflows and analyses in bacterial genomics.

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

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. Repository

GeneScreener

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

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 phylogenetic trees 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