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.
During the last decade, with the development of high throughput sequencing methods, reference laboratories and research groups studying marine mollusc diseases have advanced considerably in sequencing-based analyses. However, data management is still unconventional as the community lacks dedicated databases and tools, despite a considerable increase in data volume.
Material and methods
We therefore developed a user-friendly web-platform, called MoPSeq-DB, which references curated genomic data related to mollusc pathogens. It gives users opportunities to navigate through data, interactively visualise genomic structure and variation, provide integrated analysis tools, and allow to download data in various file formats. Since marine bivalve molluscs can be affected by viral, bacterial and eukaryotic pathogens, MoPSeq-DB is designed to be used with a large panel of genome particularities (e.g. size, architecture).
MoPSeq-DB, is an open-source tool based on the Python web-framework Django enabling convenient and fast sequencing data exploration and visualisation in an intuitive and user-friendly way, particularly for non-bioinformaticians. It has minimal hardware requirements and is easy to install, host, and update.
While MoPSeq-DB folder structure enforces systematic yet flexible storage of genomic data of bivalve mollusc pathogens, including associated metadata, the platform could easily be declined to pathogens of any other organisms. The application can be deployed using a Docker container, and runs on all modern browser engines (Firefox, Chrome, Safari).
Source code and documentation are available at https://gitlab.ifremer.fr/bioinfo/mopseq-db.
A public web server will be online at: https://mopseq-db.ifremer.fr by end 2023.