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Tools & Education

Hello fellow scientist! Welcome to our ‘Tools and Education’ section!

In MMBioIT we actively develop tools for bacterial genomics, focusing on providing software that is easy to install and use. We strongly believe in transparent and collaborative science, and therefore all our tools are completely open-source. We encourage you to try our tools and, if you dare, suggest improvements for them.

Are you a wet-labber? Are you interested in learning bioinformatics? Then you should check our Education section! You will find free courses to improve your bioinformatics skills.

Tools

Gplas

gplas is a tool to bin plasmid-predicted contigs based on sequence composition, coverage and assembly graph information. This tool extends the possibility of accurately binning predicted plasmid contigs into several discrete plasmid components.

mlplasmids

mlplasmids consists of binary classifiers to predict contigs either as plasmid-derived or chromosome-derived. It currently classifies short-read contigs as chromosomes and plasmids for Enterococcus faecium, Enterococcus faecalis, Klebsiella pneumoniae and Acinetobacter baumannii.

MetaMobilePicker

MetaMobilePicker is a computational pipeline designed to identify mobile genetic elements and antimicrobial resistance genes in metagenomics samples. Currently it identifies plasmids, insertion sequences and bacteriophages.

plasmidEC - plasmid Ensemble Classifier

plasmidEC identifies plasmid-derived contigs in E. coli. This tool combines the output of three binary classification tools and implements a majority vote system. Currently, the user can choose any combination of the following four softwares: PlaScope, Platon, RFPlasmid and mlplasmids. More softwares could be added in the future.

Bactofidia

bactofidia is a bacterial assembly and basic analysis pipeline using Snakemake and bioconda. It is currently written for paired-end Illumina data with length 250 or 150. The pipeline is written to ensure reproducibility, and creates virtual software environments with the software versions that are used for analysis.

VREfidia

VREfidia is a bacterial assembly and basic analysis pipeline for vancomycin-resistant Enterococcus faecium (VRE) using Snakemake and bioconda. It is designed for paired-end Illumina data.

Educational resources

Molecular Epidemiology of Infectious Diseases - computer practical

Three day graduate level course on molecular epidemiology teaching the command line, WGS, annotation and pangenomics.

Microbial Genomics Workshop

Three day course on microbial genomics from commandline to SNP analyses using data from the Lenski Long Term Evolution experiment.