MetaScope: An R Package for Accurate Metagenomic Taxonomic Profiling

Music City Center 

MetaScope is a novel R package designed for the rapid, accurate taxonomic profiling of metagenomic and 16S sequencing reads. MetaScope addresses a critical need for efficient and precise microbial composition analysis. Its core modules are MetaRef, which builds reference genome sequence libraries, MetaAlign, which aligns reads to the target library using Bowtie 2 or Subread aligners, MetaFilter, which filters reads that align to the host library, and MetaID, which reassigns ambiguously mapped reads to their likely genome of origin using a Bayesian model. MetaScope also offers demultiplexing and output aggregation modules to enhance functionality and integrates with the animalcules R package for downstream microbiome analysis. A novel feature is the complementary coverage plots in the MetaID module, enabling additional quality checking and improved post-processing. We evaluated MetaScope's performance with benchmarking against mock microbial communities using 16S datasets. These results demonstrate that MetaScope achieves strain-level differentiation capabilities and demonstrates high sensitivity compared to other 16S profilers.

Bayesian

Metagenomics

Microbiome

Microbial Profiling

Genomics 

Section on Statistics in Genomics and Genetics