Panache: a web browser-based viewer for linearized pangenomes.

Éloi Durant,Matthieu Conte,Mathieu Rouard,François Sabot,Tobias Marschall

doi:10.1093/bioinformatics/btab688

Abstract

MotivationPangenomics evolved since its first applications on bacteria, extending from the study of genes for a given population to the study of all of its sequences available. While multiple methods are being developed to construct pangenomes in eukaryotic species there is still a gap for efficient and user-friendly visualization tools. Emerging graph representations come with their own challenges, and linearity remains a suitable option for user-friendliness.ResultsWe introduce Panache, a tool for the visualization and exploration of linear representations of gene-based and sequence-based pangenomes. It uses a layout similar to genome browsers to display presence absence variations and additional tracks along a linear axis with a pangenomics perspective.Availability and implementationPanache is available at github.com/SouthGreenPlatform/panache under the MIT License.

Highlights

The widespread use of fast and affordable sequencing technologies unveiled how much genomic information was lost when relying on a single and unique reference genome
As reviewed in (Golicz et al, 2019), some studies handle this approach through a gene or functional annotation lens while others extend it to DNA sequences, especially when the studied organisms are eukaryotes
More tools are needed to help pangenomics to reach a broader audience within the scientific community (Computational Pan-Genomics Consortium, 2018; Golicz, Batley, et al, 2016; Tranchant‐Dubreuil et al, 2019)

Summary

Introduction

The widespread use of fast and affordable sequencing technologies unveiled how much genomic information was lost when relying on a single and unique reference genome. By leveraging data of multiple references instead, a new era of genomics emerged: Pangenomics. The current trend for sequence-based pangenomes is to use graph visualization software like Bandage (Wick et al, 2015), a general tool for navigating assembly graphs, but alternatives dedicated to pangenomes and their inner properties are yet to be refined and adopted.

Results

Conclusion