software
METAnnotatorX2
Platform for taxonomic and functional analysis of metagenomic data, short/long-read assembly and management of metagenomic contigs.
Computational Microbiology Unit
Tools
Computational resources for microbial genome, pangenome, phylogenomics, metagenomic and viromic analyses, developed and maintained by our team.
software
MEGAnnotator2
Automated pipeline for filtering, assembly, quality control and functional annotation of microbial genomes from short and long reads.
software
Bacterial ITS profiling
Species-level bacterial community profiling using the ITS region and a curated reference database.
software
Optimal Reference Strain selector
Selection of reference strains based on ecological, genomic and functional representativeness.
software
ITS profiling of bifidobacteria
Protocol and resources for bifidobacterial profiling at species and subspecies resolution.
software
ITS profiling of lactobacilli
ITS-based approach for species-level profiling of lactobacilli in complex matrices.
software
RefBifSelector
Tool for identifying local bifidobacterial strains closest to proposed reference models.
Resources
Databases
database
Microbial BioRemediation database
Curated repository of protein sequences associated with microbial degradation of organic and inorganic pollutants.
database
Integrated Probiotics Database
Integrated genomic database of probiotic strains and traits potentially involved in microbe–host interactions.
database
Probiotic Bifidobacteria Database
Genomic resource covering major bifidobacterial strains used in probiotic products.
database
Plastic Microbial BioRemediation Database
Multi-omics database of microbial genes and enzymes associated with plastic degradation.
database
Bifidobacterial T4P database
Catalogue of type IV pili loci and genes across the diversity of the genus Bifidobacterium.