There are 4 repositories under bacteria topic.
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
:floppy_disk: :page_with_curl: "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.
Hardware and software for accessible, extensible, and scalable bioreactors. Built on Raspberry Pi.
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.
A machine learning model for the prediction of optimal growth temperature of microorganisms and enzyme catalytic optima
A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
A curated list of phage related software and computational resources for phage scientists, bioinformaticians and enthusiasts.
A pipeline to identify pathogenic microorganisms from scRNA-seq raw data.
Order and orientation of complete bacterial genomes
Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)
Bacterial analysis toolbox for full ESKAPE pathogen characterization and profiling the resistome, mobilome, virulome & phylogenomics using WGS
This program is designed for annotation of antimicrobal resistance(AMR), transposon(Tn) and integron(In) in bacteria.
This project was created from Shell which allows people to download cell skins from https://agar.io.
Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]
A spatially explicit trait- and individual-based microbial systems modelling framework