We are excited to share our new tool, euka, for the robust and rapid screening of mitochondrial arthropodic and tetrapodic DNA in ancient environmental samples using pangenomics. We use the vg toolkit to build a taxon-based pangenome graph from 5847 species. The only input needed for our tool is a pre-processed FASTQ file, which we map with vg giraffe against our reference structure. The resulting alignments are post-processed by euka, using a maximum-likelihood framework and a minimum breadth of coverage filter to minimise the number of spurious alignments and provide the user with an accurate taxonomic profile of their sample. We estimate the abundance of each detected taxa with an MCMC sampling algorithm and provide these as well as a damage profile, fragment length distribution and estimated coverage.
Our goal was to develop an easy-to-use screening tool that gives the user robust results and allows them to optimise their downstream analysis. euka is available via the vgan suite for pangenomics: https://github.com/grenaud/vgan.
