Fast Whole-Genome Similarity (ANI) Estimation

Build a partitioned pangenome graph from microbial genomes

Rapid & standardized annotation of bacterial genomes & plasmids

From genomes to phenotypes: Traitar, the microbial trait analyzer

Collection of scripts for bacterial genomics

Estimate metagenomic coverage and sequence diversity

Get microbial sequence data easier and faster

MiGA: Microbial Genomes Atlas

A Python package for gene-centric taxonomic and functional classification using phylogenetic placement

A comprehensive R package for microbiome analysis.

Tools for phylogenetic data analysis including visualization and cluster-computing support.

A Java Desktop application with a graphical user interface for the discovery of colinear syntenic blocks across thousands microbial genomes

An easy way of MLSTyping your genomes in R.

A grammar for describing microbial genotypes and phenotypes

Comparative TraDIS analysis

In silico serotype prediction for Listeria monocytogenes

Data-centric bioinformatics environment for virus sequence data, implemented in Java

A metagenome annotation workflow for UBC's Microbiology 405 course, Bioinformatics

Simulate pangenomes according to the IMG + Neutral models

Bioinformatics pipeline used for the RCPA WGS PTP

Collection of 1069 Escherichia coli virulence factors

🦠📇 Compare microbial assemblies

A comprehensive and intuitive encapsulated OO class system for analyzing bacterial pangenomes in R.

Sequence Matching fOr REpiratory Diseases, SMORE'D, is a command-line sequence classification tool tailored to meet the needs of the Undiagnosed Respiratory Disease Outbreak (URDO) branch at CDC. SMORE'D is a k-mer based classification tool capable of rapidly classifying read sequences generated by multi-pathogen detection platforms.

Fast microbial species identification (16S rRNA gene-based approach) and contamination check using whole genome assemblies

Call core SNPs agains a reference genome for a set of bacterial isolates, and build a phylogenetic tree based on the core-genome SNP information.

Research on position-dependent hydrogen bonds per codon

Remove host reads from a microbial pathogen sequence dataset by aligning against a reference genome. Verify that the reads were removed using Kraken2/Bracken

Make mutated copies of DNA components in BioPython