Pathogen surveillance and diagnostic methods are constantly evolving. Sequencing can provide critical information to diagnose diseases and inform control and mitigation strategies by identifying genetically distinct pathogen variants that may have different host reservoir species or geographic distributions. However, most reference laboratories for marine mollusc diseases lack the resources or expertise for sequencing and data analysis. We therefore developed a user-friendly web-application, called MoPSeq-DB.

MoPSeq-DB, is an open-source tool based on the Python web-framework Django. It is deployed through a Docker container, on a dedicated server. Genomes as well as their annotations and variations are stored and organised in a folder architecture designed to make files available to users. Annotation and variation files are parsed and summarised in interactive Javascript graphs using Python and Bash scripts. Then, a pre-built phylogenetic tree, based on all genomes included in the database, can also be visualised and handled. 

MoPSeq-DB web-platform references curated genomic data related to mollusc pathogens, gives users opportunities to interactively visualise data and provides integrated analysis tools. The database currently primary focuses on the OsHV-1 virus, but will later be completed with other mollusc pathogens such as the bacterium Vibrio aestuarianus or the protozoa Marteilia refringens.

This project will provide robust bases to unify all sequence-based work related to mollusc pathogens and will offer unprecedented opportunities to carry out monitoring and diagnosis in near-real time. MoPSeq-DB is, to our knowledge, the first comparative genome browser dedicated to mollusc pathogens. It automates commonly used bioinformatics workflows, enabling convenient and fast data exploration, particularly for non-bioinformaticians, in an intuitive and user-friendly way. It has minimal hardware requirements and is easy to install, host, and update. MoPSeq-DB folder structure enforces systematic yet flexible storage of genomic data of mollusc pathogens, including associated metadata. The platform could easily be declined to other pathogens.