Evaluation of variant calling for cpn60 barcode sequence-based microbiome profiling.

ABSTRACT: Amplification and sequencing of conserved genetic barcodes such as the cpn60 gene is a common approach to determining the taxonomic composition of microbiomes. Exact sequence variant calling has been proposed as an alternative to previously established methods for aggregation of sequence reads into operational taxonomic units (OTU). We investigated the utility of variant calling for cpn60 barcode sequences and determined the minimum sequence length required to provide species-level resolution. Sequence data from the 5´ region of the cpn60 barcode amplified from the human vaginal microbiome (n = 45), and a mock community were used to compare variant calling to de novo assembly of reads, and mapping to a reference sequence database in terms of number of OTU formed, and overall community comp

SUBMITTER: Vancuren SJ 

PROVIDER: S-EPMC7347135 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature