📦 🐳 Dockerfiles and documentation on tools for public health bioinformatics

🤖 Just a command runner

Python tool for converting files and office documents to Markdown.

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

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

QC cutoffs for different genomes.

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…

Scripts and reference files to type Group A Streptococcus

Download alleles and profiles from PubMLST and BIGSdb Pasteur

MycoSNP: Whole Genome Sequencing Analysis of Fungal Isolates

tenzing: documening contributorship with CRediT

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

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

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

Simple-to-use interactive comparison of two bacterial genomes

Tools And ggplot Extensions For Infectious Disease Surveillance And Outbreak Investigation

The Pathogenwatch Vibrio cholerae genotyping tool

Create beautiful Gantt charts with ggplot2

Alignment viewer for linux terminal

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

AMR inference for Mtb - cousin to abriTAMR

Real time and remote MCMC trace monitoring with BEASTIARY.

Bioinformatics tool to find integrons in bacterial genomes

emm Automatic Isolate Labeller

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

Neptune: Genomic Signature Discovery

Code sharing for the ciprofloxacin prediction research

Applied Computational Genomics Course at UU: Spring 2020