Struo

Struo builds custom databases for metagenome profilers by automating the acquisition of microbial genomes from public repositories to improve taxonomic and functional profiling of metagenomic sequencing data.

Key Features:

• Modular design: Modular pipeline architecture that can be modified or extended to accommodate different database construction steps.
• Automated genome acquisition: Automates fetching microbial genomes from public repositories to incorporate recent genome additions.
• Custom database construction: Constructs databases tailored for various metagenome profilers to reflect selected genome sets.
• Broad representation: Incorporates novel genomes to expand representation of known microbial diversity within reference databases.

Scientific Applications:

• Increased mappability: Improves read mappability for both synthetic and real metagenome datasets by including up-to-date genomes.
• Taxonomic profiling: Enhances taxonomic profiling of microbial communities from metagenomic sequencing data.
• Functional profiling: Enhances functional profiling by providing updated gene and genome references for read mapping.
• Reference database updating: Enables construction of current reference databases for metagenomic analyses.

Methodology:

Automated acquisition of genomes from public repositories and construction of custom databases implemented as a modular pipeline that incorporates novel genomes into profiler-specific reference sets.