Tools

GitHub links to open-source software and analysis tools, developed as part of my research in pangenomics and machine learning to study microbial epidemiology and evolution.

python rust r c++ snakemake genomics pangenomics simulation machine-learning

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ggCaller Graph-based gene caller for pangenomes

A pangenome-graph-based gene caller for bacterial genomes.

c++ python pangenomics

ggCallaroo ggCaller + Panaroo + Bakta pipeline

A Snakemake pipeline combining ggCaller, Panaroo, and Bakta for pangenome analysis.

python snakemake pangenomics

PanBART Long-context encoder-decoder for pangenomes

A long-context encoder-decoder package for pangenomes.

python machine-learning pangenomics

PansimNuc Nucleotide-level pangenome simulator

A nucleotide-level pangenome simulator written in Rust.

rust simulation pangenomics

PopPUNK-mod Fitting models of pangenome evolution in bacteria

Scalable models of pangenome evolution in bacteria, fitting to PopPUNK data using Approximate Bayesian Computation.

python pangenomics modelling simulation

Pansim Bacterial pangenome simulator

A pangenome simulator for bacterial gene presence/absence.

rust simulation pangenomics

CELEBRIMBOR Pangenomes from metagenomes

A tool for pangenome analysis from metagenome assembled genomes (MAGs).

snakemake pangenomics metagenomics

GNASTy Graph-based Nanopore Adaptive Sampling Typing

A pangenome graph-based tool for adaptive sampling in nanopore sequencing.

python nanopore adaptive-sampling

ExpEvoAnalyzer Experimental evolution analysis workflow

A workflow to analyse experimental evolution data using read alignment, variant calling and annotation.

snakemake python experimental-evolution genomics

orthosynt Synteny-based orthologue analysis

A Python script to analyse Orthofinder results and determine orthologues based on synteny.

python clustering

WTBcluster Large-scale protein clustering workflow

A Snakemake workflow for clustering billions of proteins.

python snakemake clustering

ATB_tree AllTheBacteria tree construction

A set of scripts for constructing trees from millions of genomes.

python phylogenetics

BacCorpusWF Training data generation for Bacformer v2

Scripts for generating training datasets for Bacformer v2.

python snakemake machine-learning

unitig_caller Counting unitigs in a de Bruijn graph

A tool for counting unitigs in a de Bruijn graph for microbial GWAS.

c++ python pangenomics

pangenome_LLM Language models for pangenomics

Scripts for applying large language models to pangenome analysis.

python machine-learning pangenomics

locus_cutter Target sequence cutting from genomes

A tool for identifying and cutting target sequences from a genome.

python genomics

adaptive_sampling_scripts Scripts for adaptive sampling in nanopore sequencing

Scripts to aid in analysis of adaptive sampling experiments in nanopore sequencing.

python nanopore adaptive-sampling

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