GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
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Updated
May 17, 2024 - Python
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
Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.
SEER, reimplemented in python 🐍🔮
Hardware and software for accessible, extensible, and scalable bioreactors. Built on Raspberry Pi.
PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)
A machine learning model for the prediction of optimal growth temperature of microorganisms and enzyme catalytic optima
Accurate, resource-frugal and deterministic DNA sequence classifier.
🦠📇 Genomes to report pipeline - for bacteria and archaea
Order and orientation of complete bacterial genomes
A pipeline to identify pathogenic microorganisms from scRNA-seq raw data.
Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)
A spatially explicit trait- and individual-based microbial systems modelling framework
Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]
Evaluating Nanopore-based bacterial variant calling
Software to predict the occurence of programmed ribosomal frameshifting in bacterial, phage, and viral genomes
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