The Pathogenwatch Vibrio cholerae genotyping tool

Tools And ggplot Extensions For Infectious Disease Surveillance And Outbreak Investigation

Neptune: Genomic Signature Discovery

Nextflow Pipeline for processing Streptococcus pneumoniae sequencing raw reads (FASTQ files) by the GPS Project (Global Pneumococcal Sequencing Project)

Download alleles and profiles from PubMLST and BIGSdb Pasteur

Applied Computational Genomics Course at UU: Spring 2020

Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by using evidence-based methods, as described in https://d…

A DRAFT, early stage book on snakemake.

A toolkit for exploring prokaryotic methylation and base modifications in nanopore sequencing

AMR inference for Mtb - cousin to abriTAMR

CDCgov/mycosnp-nf

Follow up to Grace Blackwell's 661k dataset, for 2023

Alignment viewer for linux terminal

Create beautiful Gantt charts with ggplot2

A practical cross-platform command-line tool for safely batch renaming files/directories via regular expression

A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data

📦 🐳 Dockerfiles and documentation on tools for public health bioinformatics

A curated list of awesome self-hosted GitHub Action runners in a large comparison matrix

emm Automatic Isolate Labeller

Scripts and reference files to type Group A Streptococcus

Basic assembly workflow for NRLBM

Real time and remote MCMC trace monitoring with BEASTIARY.

benchmarkig phylogenetic workflows for E.coli K12 whole genome Written by Niek Huijsmans

Code sharing for the ciprofloxacin prediction research

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

🛁 Clean Code concepts adapted for Python