microbiology
There are 199 repositories under microbiology topic.
microbiome/microbiome
microbiome R package
MrOlm/drep
Rapid comparison and dereplication of genomes
moshi4/pyGenomeViz
A genome visualization python package for comparative genomics
labgem/PPanGGOLiN
Build a partitioned pangenome graph from microbial genomes
oschwengers/platon
Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.
oschwengers/referenceseeker
Rapid determination of appropriate reference genomes.
msberends/AMR
Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by using evidence-based methods, as described in https://doi.org/10.18637/jss.v104.i03.
qgeissmann/OpenCFU
An easy-to-use C++ application to count bacterial colonies (i.e. CFU).
rdpstaff/RDPTools
Collection of commonly used RDP Tools for easy building
vinuesa/get_phylomarkers
A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches
EngqvistLab/Tome
A machine learning model for the prediction of optimal growth temperature of microorganisms and enzyme catalytic optima
aleimba/bac-genomics-scripts
Collection of scripts for bacterial genomics
BU-ISCIII/plasmidID
PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification.
dmnfarrell/teaching
scripts and notes for learning
Geo-omics/scripts
Metagenomic pipeline and other general scripts used in the lab.
telatin/gan
📜 the Great Automatic Nomenclator — The Next Million Names for Archaea and Bacteria
chasemc/IDBacApp
A MALDI Mass Spectrometry Bioinformatics Platform
JTFouquier/ghost-tree
creating hybrid-gene phylogenetic trees for diversity analyses
jlumpe/gambit
A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.
ewissel/hAMRoaster
hAMRoaster is an analysis pipeline that can compare the output of tools for detecting AMR genes and provide metrics of their performance
dr-joe-wirth/phantasm
PHANTASM: PHylogenomic ANalyses for the TAxonomy and Systematics of Microbes
vallenderlab/MicrobiomeR
A comprehensive and customizable R package for microbiome analysis.
frubino/mgkit
MGKit: Metagenomics Framework
mshamash/OnePetri
Accelerate common Petri dish assays with AI.
microbialman/DDotCounter
Simple counting of bacterial colonies from pictures of plates.
TIBHannover/BacDiveR
Inofficial R client for the DSMZ's Bacterial Diversity Metadatabase (former contact: @katrinleinweber). https://api.bacdive.dsmz.de/client_examples seems to be the official alternatives.
moshi4/pybarrnap
Python implementation of barrnap (Bacterial ribosomal RNA predictor)
majsylw/microbial-counting-review
A list of useful resources in the microbial colony classification and detection, such as datasets, papers, links to projects
NadjaKry/WGS_pipeline
Bacterial whole genome sequencing (WGS) analysis
jonasoh/spiro
SPIRO is a Smart Plate Imaging Robot
m-jahn/genome-scale-models
Genome scale metabolic models in SBML format
genotoul-bioinfo/Binette
A fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools.
mshamash/OnePetri-models
Repository containing trained YOLOv5 object detection models used within OnePetri for Petri dish and plaque detection.
schwanbeck/YSMR
Bacterial video tracking & analysis
USDA-ARS-GBRU/GuideMaker
GuideMaker: Software to design CRISPR-Cas guide RNA pools in non-model genomes