Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

✂️ ⚡ Rapid haploid variant calling and core genome alignment

Build a partitioned pangenome graph from microbial genomes

Pan-genome wide association studies

PhenoPixel: A web-based bioimage analysis platform for bacterial single-cell microscopy analytics.

BSR-Based Allele Calling Algorithm

Hardware and software for accessible, extensible, and scalable bioreactors. Built on Raspberry Pi.

💾 📃 "Reads to report" for public health and clinical microbiology

SEER, reimplemented in python 🐍🔮

GET_HOMOLOGUES: a versatile software package for pan-genome analysis

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

A bioinformatic toolkit to align genome assemblies into pangenome graphs

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

A scalable bacterial genome assembly, annotation and analysis pipeline

Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.

🦠🧬🧑‍💻📇 Microbial genomes-to-report pipeline

A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

A machine learning model for the prediction of optimal growth temperature of microorganisms and enzyme catalytic optima

A curated list of phage related software and computational resources for phage scientists, bioinformaticians and enthusiasts.