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
Whole Genome Sequencing
Gplasgplas 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.
mlplasmidsmlplasmids 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.
plasmidECplasmidEC identifies plasmid-derived contigs in all bacterial species. 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: Centrifuge, Platon, RFPlasmid and mlplasmids.
Bactofidiabactofidia 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.
ClonalTrakerClonalTraker is a tool to compare any two vancomycin-resistant Enterococcus faecium (VRE), and the genomic context of the van operon.
Metagenomics
MetaMobilePickerMetaMobilePicker 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.
TourmalineTourmaline is an amplicon sequence processing workflow for Illumina sequence data developed by the Nacional Oceanic and Atmospheric Administration that uses QIIME 2 and the software packages it wraps. We modified this package to fit our sequencing data and system requirements.
Educational resources
Molecular Epidemiology of Infectious Diseases - computer practicalThree day graduate level course on molecular epidemiology teaching the command line, WGS, annotation and pangenomics.
Microbial Genomics WorkshopThree day course on microbial genomics from commandline to SNP analyses using data from the Lenski Long Term Evolution experiment.