EPIK: Precise and scalable evolutionary placement with informative k-mers
N. Romashchenko, B. Linard, F. Pardi, E. Rivals.
Bioinformatics, in press
EPIK is a program dedicated to "Phylogenetic Placement" (PP) of metagenomic or metabarcoding reads on a reference tree.
It is similar in spirit and technically the successor of
RAPPAS (Linard et al. 2020).
EPIK achieves identical or slightly better accuracy than RAPPAS and outperforms it in speed and flexibility.
In many aspects the documentation of RAPPAS remains valid.
EPIK takes as input a file containing database of phylo-k-mers built with
IPK and a set of reads to place on the related phylogeny. It works for nucleotidic and amino-acid query sequences.
EPIK can filter the database to load only the most informative phylo-k-mers, which reduces the memory usage.
EPIK can also run in parallel.
Keywords
Phylogenetic placement, metabarcoding, taxonomic identification, NGS, software
The workflow combining IPK, to precompute the index, and then EPIK, to perform the placement of the reads.