Pangenomic read mapping

In modern genomics, mapping reads to a single reference genome is common practice. However, a reference genome does not necessarily accurately represent a population or species and as a result a substantial percentage of reads often cannot be mapped. A number of graph-based variation-aware mapping methods have recently been proposed to remedy this. Here, we propose an alternative multi-reference approach, which aligns reads to large collections of genomes simultaneously. Our approach, an extension to our pangenomics suite PanTools (https://git.wur.nl/bioinformatics/pantools), is as accurate as state-of the-art tools but more efficient on large numbers of genomes. We successfully applied PanTools to map genomic and metagenomic reads to large collections of viral, archaeal, bacterial, fungal and plant genomes.