TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution.

ABSTRACT: Taxonomy assignment of freshwater microbial communities is limited by the minimally curated phylogenies used for large taxonomy databases. Here we introduce TaxAss, a taxonomy assignment workflow that classifies 16S rRNA gene amplicon data using two taxonomy reference databases: a large comprehensive database and a small ecosystem-specific database rigorously curated by scientists within a field. We applied TaxAss to five different freshwater data sets using the comprehensive SILVA database and the freshwater-specific FreshTrain database. TaxAss increased the percentage of the data set classified compared to using only SILVA, especially at fine-resolution family to species taxon levels, while across the freshwater test data sets classifications increased by as much as 11 to 40% of total re

SUBMITTER: Rohwer RR 

PROVIDER: S-EPMC6126143 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature