SCRAPP: A tool to assess the diversity of microbial samples from phylogenetic placements.

ABSTRACT: Microbial ecology research is currently driven by the continuously decreasing cost of DNA sequencing and the improving accuracy of data analysis methods. One such analysis method is phylogenetic placement, which establishes the phylogenetic identity of the anonymous environmental sequences in a sample by means of a given phylogenetic reference tree. However, assessing the diversity of a sample remains challenging, as traditional methods do not scale well with the increasing data volumes and/or do not leverage the phylogenetic placement information. Here, we present scrapp, a highly parallel and scalable tool that uses a molecular species delimitation algorithm to quantify the diversity distribution over the reference phylogeny for a given phylogenetic placement of the sample. scrapp employ

SUBMITTER: Barbera P 

PROVIDER: S-EPMC7756409 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature