RAPPAS
Résumé
RAPPAS: Rapid Alignment-free Phylogenetic Placement via Ancestral Sequences RAPPAS is a program dedicated to "Phylogenetic Placement" (PP) of metagenomic or metabarcoding reads on a reference tree. As apposed to previous PP programs, RAPPAS is based on the phylo-kmers idea, detailed in tis manuscript and uses a 2 step approach divided into a) the database build, and b) the placement itself. This README contains short instructions to build and launch RAPPAS. You will find more detailed instructions, test datasets, pre-built databases and tutorials and discussions related to phylogenetic placement on the wiki page (https://github.com/phylo42/RAPPAS/wiki).
Cite lirmm-02410441 Article Benjamin Linard, Krister M. Swenson, Fabio Pardi. Rapid alignment-free phylogenetic identification of metagenomic sequences. Bioinformatics, 2019, 35 (18), pp.3303-3312. ⟨10.1093/bioinformatics/btz068⟩. ⟨lirmm-02410441⟩
Cite 10.1093/bioinformatics/btz068 Autre Linard, B., Swenson, K., & Pardi, F. (2019). Rapid alignment-free phylogenetic identification of metagenomic sequences. Bioinformatics, 35(18), 3303–3312. https://doi.org/10.1093/bioinformatics/btz068
