GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
✂️ ⚡ Rapid haploid variant calling and core genome alignment
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
Build a partitioned pangenome graph from microbial genomes
Pan-genome wide association studies
💾 📃 "Reads to report" for public health and clinical microbiology
BSR-Based Allele Calling Algorithm
SEER, reimplemented in python 🐍🔮
Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.
GET_HOMOLOGUES: a versatile software package for pan-genome analysis
Hardware and software for accessible, extensible, and scalable bioreactors. Built on Raspberry Pi.
PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)
A bioinformatic toolkit to align genome assemblies into pangenome graphs
A scalable bacterial genome assembly, annotation and analysis pipeline
🦠📇 Microbial genomes-to-report pipeline
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.
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