Loculus is a software package to power microbial genomic databases. Loculus aims to be widely useful to groups who need to manage sequencing data. It can be used by small public health or research laboratories with a few members for storing their own, internal data as well as by international databases facilitating global pathogen sequence sharing.

Nextclade aligns viral genomes to a reference sequence, calculates several quality control (QC) metrics, assigns sequences to a clade or lineage, and identifies changes in the viral proteins relative to the reference sequence, enabling an easy, fast, and decentralized analysis of initial data. Nextclade is available as a command-line tool and as a web application with completely client based processing, meaning that sequence data doesn’t leave the user’s browser.

ViralZone is a web resource for all viral genus and families, providing general molecular and epidemiological information, along with virion and genome figures. Each virus or family page gives an easy access to UniProtKB/Swiss-Prot viral protein entries.

Foldtree creates phylogenetic trees from protein structures using Foldseek to align protein structures and generate distance matrices for tree construction.

BEAST 2 is an open source software tool and platform designed for Markov chain Monte Carlo (MCMC)-based Bayesian inference of phylogenetic trees and associated population-level (i.e. phylodynamic) parameters from (primarily) genetic sequence data under a large variety of specific models.

IMMense (IMM Extended Nextflow Sequencing Environment) is a Nextflow pipeline to analyze bacterial and fungal genomes. It covers genome assembly and annotation, species identification, resistance and virulence gene analysis as well as specific modules for selected species.

Nextstrain is an open-source project to harness the scientific and public health potential of pathogen genome data. We provide a continually-updated view of publicly available data alongside powerful analytic and visualization tools for use by the community. Our goal is to aid epidemiological understanding and improve outbreak response.

V-pipe is the bioinformatics pipeline that integrates various open-source software packages for assessing viral genetic diversity from next-generation sequencing (NGS) data derived from intra-host virus populations.

Starting from work done previously, such as the ELIXIR-CONVERGE project, we have developed a Capacity Framework to support the implementation of FAIR pathogen data infrastructures and metadata standards.