Speaker
Description
Viral sequencing data are collected, stored, and processed by a wide range of entities, from individual scientists and laboratories to large consortia and global databases. Yet, there has been a lack of a general, reusable software for managing pathogen sequencing data. During the SARS-CoV-2 pandemic, when many new laboratories and consortia started sequencing or analyzing data, they relied on spreadsheets (e.g., Excel) or had to develop new data management tools (e.g., MAJORA by COG-UK, SPSP in Switzerland). Simultaneously, major international databases such as the INSDC and GISAID had to extend their platforms to meet new demands.
Our project, Loculus, addresses this gap. Loculus is an open-source, general-purpose software package designed for sharing, maintaining, and accessing pathogen genetic sequencing data. It is highly configurable, supporting supporting versatile metadata schema, and pathogen-agnostic, accommodating both single- and multi-segmented genomes. Loculus features user-friendly interfaces and APIs for data submission and rapid querying, collaborative group-based data management, and versioning to track data changes. Its modular architecture offers a high degree of flexibility, enabling customization for diverse use cases. Loculus can be used with the preprocessing pipeline that we have developed, using Nextclade for alignment, mutation calling and quality checks, just by specifying a Nextclade dataset, but it is also easy to develop and integrate custom pipelines.
In our presentation, we will showcase the architecture of Loculus and demonstrate its wide range of use cases through real-world applications, including Pathoplexus (a global database for sharing viral sequences) and GenSpectrum (a variant analysis dashboard that uses Loculus for data management), as well as prototype instances for managing multi-pathogen panel sequencing data obtained from patient samples and results from wastewater samples.
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