PanLoki – Workflow and web interface to the pangenomic software Genset

Abstract

The advancement and reduced cost of whole genome sequencing allow sequencing of a representative of the same species multiple times or multiple members of a group or a population within a species of higher taxonomic level. This availability of data makes it possible to replace the linear reference genome with a pangenome of closely related organisms to represent a larger genetic diversity of these organisms. A pangenome is a richer data structure consisting of multiple genomes where homologous genes get clustered into gene sets. The gene sets are assigned a certain pangenome characteristic based on distribution within the pangenome such as core, soft-core, shell, or cloud. Bacterial pangenomes can be used to resolve the ecological role of different groups and their niches, it can help explain host-pathogen interactions of bacteria harmful to humans, create vaccines against them with the reverse vaccinology approach, or identify industrially relevant enzymes. Examples of such enzymes are thermostable enzymes obtained from thermophilic bacteria.This thesis presents PanLoki, a web-based, visual, and interactive approach to generating and exploring a pangenome. PanLoki is a linear workflow in seven interconnected phases, guiding the user through the process of generating and investigating the pangenome, with a graphical interface. It focuses on being user-friendly, and that its results are shareable and reproducible. The PanLoki software was created to serve as the accompanying web app for the Java-based software Genset, a stand-alone pangenome analysis tool (Stefánsson and Hreggvidsson, unpublished).Other available bacterial pangenome pipelines differ from PanLoki by being command-line tools that generate result tables and static images. This makes them hard to use without programming and command line knowledge. PanLoki furthermore removes the need to jump between different bioinformatics tools and services to obtain and visualize the data needed for creating a pangenome.The user loads genome sequences into PanLoki and the workflow implements all the steps necessary to create a pangenome. It clusters homologous genes of the different genomes into gene sets and assigns pangenomic characteristics to each gene set. PanLoki provides additional features and visualizations to explore the pangenome and its gene sets.PanLoki was evaluated on two groups of thermophilic bacteria to showcase its usage and functionality.This thesis presents to the knowledge of the author the first web-based, pangenome explorer that enables researchers to generate a bacterial pangenome easily and quickly and explore the results visually and interactively in the same program.