euka: Robust detection of eukaryotic taxa from modern and ancient environmental DNA using pangenomic reference graphs

Ancient environmental DNA (eDNA) is a crucial source of in-formation for past environmental reconstruction. However, the com-putational analysis of ancient eDNA involves not only the inherited challenges of ancient DNA (aDNA) but also the typical difficulties of eDNA samples, such as taxonomic identification and abundance esti-mation of identified taxonomic groups. Current methods for ancient eDNA fall into those that only perform mapping followed by taxo-nomic identification and those that purport to do abundance estima-tion. The former leaves abundance estimates to users, while methods for the latter are not designed for large metagenomic datasets and are often imprecise and challenging to use.