The Vizitig pangenome and pantranscriptome explorer

Abstract

Vizitig is the first platform for real-time exploration and querying of DNA and RNA sequence de Bruijn graphs across many samples, unifying visualization, metadata, and flexible search. It constructs compacted colored de Bruijn graphs from raw sequencing reads and reference sequences, then provides an interactive web interface for graph exploration. It integrates raw and reference-based data, handles complex variation, and provides a human-readable feature-based (also referred to as metadata) query language with scalable graph loading. Its domain-specific query language supports composable searches combining sequences of arbitrary size, genomic features such as gene or exon identifiers, and experimental factors such as sample identifier or abundance thresholds. On-demand subgraph loading retrieves only regions of interest, enabling interactive ex- ploration of large datasets in the graphical user interface without loading the entire graph into memory. We demonstrate Vizitig's capabilities through case studies in pantranscriptomics and pangenomics. In pantranscriptomics, we recover fusion transcript breakpoints on long and short reads. In pangenomics, we explore sequence variations across yeast, rice, nematode, and human pangenomes. Vizitig scales from small virus genomes to human-scale pangenomes (our largest experiment comprises up to 20 assembled human haplotypes, on a laptop). Vizitig enables fast, reproducible analysis in both pangenomics and pantranscriptomics while providing a deployable and user-friendly working environment.