Rapid alignment-free phylogenetic identification of metagenomic sequences

Motivation Taxonomic classification is at the core of environmental DNA analysis. When a phylogenetic tree can be built as a prior hypothesis to such classification, “Phylogenetic placement” (PP) provides the most informative type of classification because each query sequence is assigned to its putative origin in the tree. This is useful whenever precision is sought (e.g. in diagnostics). However, likelihood-based PP algorithms struggle to scale with the ever increasing throughputs of DNA sequencing. Results We have developed RAPPAS (Rapid Alignment-free Phylogenetic Placement via Ancestral Sequences) which uses an alignment-free approach removing the hurdle of query sequence alignment as a preliminary step to PP. Our approach relies on the precomputation of a database of k-mers present with non-negligible probability in the relatives of the reference sequences. The placement is performed by inspecting the stored phylogenetic origins of the k-mers in the query, and their probabilities. The database can be reused for the analysis of several different metagenomes. Experiments show that the first implementation of RAPPAS is already faster than the previous likelihood-based PP algorithms, while keeping similar accuracy for short reads. RAPPAS scales PP to the era of routine metagenomic diagnostics. Availability Program and sources freely available for download at gite.lirmm.fr/linard/RAPPAS. Contact benjamin.linard@lirmm.fr