MetaGaAP: A Novel Pipeline to Estimate Community Composition and Abundance from Non-Model Sequence Data.

ABSTRACT: Next generation sequencing and bioinformatic approaches are increasingly used to quantify microorganisms within populations by analysis of 'meta-barcode' data. This approach relies on comparison of amplicon sequences of 'barcode' regions from a population with public-domain databases of reference sequences. However, for many organisms relevant 'barcode' regions may not have been identified and large databases of reference sequences may not be available. A workflow and software pipeline, 'MetaGaAP,' was developed to identify and quantify genotypes through four steps: shotgun sequencing and identification of polymorphisms in a metapopulation to identify custom 'barcode' regions of less than 30 polymorphisms within the span of a single 'read', amplification and sequencing of the 'barcode', ge

SUBMITTER: Noune C 

PROVIDER: S-EPMC5372007 | biostudies-literature | 2017 Feb

REPOSITORIES: biostudies-literature