Stars
Mashania: identify prokaryotes and find their closest relatives based on ANI
🧬 gget enables efficient querying of genomic reference databases
A dependency-free large (+2500) collection of colormaps and palettes for Python 🎨
All The Bacteria CLI — query 3.2M bacterial genomes (AMR, MLST, assemblies, metadata) from the terminal
A genome diagram generator for microbes and organelles
Various Dockerfiles I use on the desktop and on servers.
Fast pairwise transmission inference from single genome and/or metagenomic data
A Nextflow pipeline for fast and accurate SNP distance estimation from WGS read data or genome assemblies
This is a Shiny app for quantifying the benefit versus cost of whole genome sequencing (WGS) for three foodborne pathogens.
quick qc on long-read alignment files. Show read-length and depth distributions
a long read simulator that can imitate many types of read problems
GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered polymorphisms in read sets using genome-graphs.
Download FASTQ files from SRA or ENA repositories.
An automated GitHub Actions workflow for creating up-to-date fungal mash sketch databases
An interactive tool for visualizing pathogen transmission networks from genomic sequence data
Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
Visualising data frames as funky heatmaps 📊
Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
A Python package for obtaining, parsing and exploring biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)
The AMD Mountain Region Bioinformatics Code Club is a 30-minute virtual session designed for public health professionals who want to strengthen their bioinformatics skills. Each session is hands-on…
A snakelike pipeline combining ggCaller and Panaroo.