PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

RStudio add-in to make plots interactively with ggplot2

Pipeline to simulate the evolution of genome sequences of MTB under different conditions

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

Population analysis PIPEline 🛠🧬

Curated list of software tools for various aspects of prokaryote genomic analyses

Archive of Online Practical Materials for the book of Modern Phylogenetic Comparative Methods (ed. Garamszegi, 2014)

📦 🐳 Dockerfiles and documentation on tools for public health bioinformatics

Jupyter Notebooks used in data analysis for "In-host population dynamics of Mycobacterium tuberculosis complex during active disease" (Vargas et al. 2021)

Jupyter Notebooks used in data analysis for "The role of epistasis in amikacin, kanamycin, bedaquiline, and clofazimine resistance in Mycobacterium tuberculosis complex" (Vargas et al. 2021)

r package for cartogram creation

Nextflow training material

This tutorial uses QGIS 3 to teach the basics of desktop mapping software for beginners with no previous mapping experience.

Maps following the #MapPromptMonday social mapping prompts

📊 Path to a free self-taught education in Data Science!

The official repository for the EuroCrops dataset.

Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data

A repository for GitHub class

nextflow pipeline for analyzing Mycobacterium bovis genomes

A snakemake workflow for WGS-based tuberculosis transmission analysis

Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data

A set of scripts for calculating pairwise SNP distance