GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
Build a partitioned pangenome graph from microbial genomes
Pan-genome wide association studies
SEER, reimplemented in python 🐍🔮
Hardware and software for accessible, extensible, and scalable bioreactors. Built on Raspberry Pi.
Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.
PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)
A machine learning model for the prediction of optimal growth temperature of microorganisms and enzyme catalytic optima
🦠📇 Microbial genomes-to-report pipeline
Accurate, resource-frugal and deterministic DNA sequence classifier.
Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)
Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]
Order and orientation of complete bacterial genomes
A pipeline to identify pathogenic microorganisms from scRNA-seq raw data.
Evaluating Nanopore-based bacterial variant calling
A tool to detect acquired AMR genes directly from long read sequencing data.
A spatially explicit trait- and individual-based microbial systems modelling framework
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