Collection of commonly used RDP Tools for easy building
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Updated
Jun 8, 2023 - Makefile
Collection of commonly used RDP Tools for easy building
microbiome R package
Rapid comparison and dereplication of genomes
Collection of scripts for bacterial genomics
An easy-to-use C++ application to count bacterial colonies (i.e. CFU).
scripts and notes for learning
Build a partitioned pangenome graph from microbial genomes
Metagenomic pipeline and other general scripts used in the lab.
creating hybrid-gene phylogenetic trees for diversity analyses
A genome visualization python package for comparative genomics
Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.
A machine learning model for the prediction of optimal growth temperature of microorganisms and enzyme catalytic optima
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.
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.
A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches
Pipelines dealing with high throughput sequencing data for microbiology diagnostic procedures. Documentation available at http://metagenlabdiag-pipelines.readthedocs.io/en/latest/ and Docker images at https://hub.docker.com/r/metagenlab/diag_pipelines/.
PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification.
SPIRO is a Smart Plate Imaging Robot
A MALDI Mass Spectrometry Bioinformatics Platform
Genome scale metabolic models in SBML format
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