🤖 Just a command runner

QC cutoffs for different genomes.

Python tool for converting files and office documents to Markdown.

tenzing: documening contributorship with CRediT

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)

Simple-to-use interactive comparison of two bacterial genomes

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

MycoSNP: Whole Genome Sequencing Analysis of Fungal Isolates

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.