SpeciateIT and vSpeciateDB: novel, fast, and accurate per sequence 16S rRNA gene taxonomic classification of vaginal microbiota.

ABSTRACT:

Background

Clustering of sequences into operational taxonomic units (OTUs) and denoising methods are a mainstream stopgap to taxonomically classifying large numbers of 16S rRNA gene sequences. Environment-specific reference databases generally yield optimal taxonomic assignment.

Results

We developed SpeciateIT, a novel taxonomic classification tool which rapidly and accurately classifies individual amplicon sequences ( https://github.com/Ravel-Laboratory/speciateIT ). We also present vSpeciateDB, a custom reference database for the taxonomic classification of 16S rRNA gene amplicon sequences from vaginal microbiota. We show that SpeciateIT requires minimal computational resources relative to other algorithms and, when combined with vSpeciateDB, affords accurate species level

SUBMITTER: Holm JB 

PROVIDER: S-EPMC11437924 | biostudies-literature | 2024 Sep

REPOSITORIES: biostudies-literature