MetaWorks

MetaWorks processes multi-marker metabarcoding data to generate taxonomic assignments for biodiversity assessment across microbes, fungi, and animals.

Key Features:

• Workflow Automation with Snakemake: Uses Snakemake to automate workflows and enable scalability across computational environments.
• Comprehensive Marker Support: Supports COI (eukaryotes), rbcL (eukaryotes, diatoms), ITS (fungi and plants), 16S (prokaryotes), 18S (eukaryotes, diatoms), 12S (fish), and 28S (fungi) for multi-taxa metabarcoding.
• Conda Environment: Provides a Conda environment for managing program dependencies and reproducible software stacks.
• Taxonomic Assignment with RDP Classifier: Uses the RDP classifier's naive Bayesian method to assign taxonomy with statistical support at each rank.
• Multiple Processing Workflows: Offers exact sequence variant assignment, operational taxonomic unit (OTU) generation, and single-read processing workflows.
• ITS Region Handling: Trims flanking conserved rRNA gene regions and removes pseudogenes for ITS marker processing.
• Extended RDP Support: Extends RDP classifier support to additional markers including COI (animals) and rbcL (eukaryotes, land plants, diatoms).

Scientific Applications:

• Multi-domain biodiversity assessment: Produces taxonomic inventories across microbes, fungi, and animals using multi-marker metabarcoding.
• Molecular ecology: Supports molecular ecology analyses that require taxonomic assignment of metabarcodes.
• Regulatory and industrial biomonitoring: Provides harmonized processing for biomonitoring applications in regulatory and industrial contexts.

Methodology:

Processes demultiplexed Illumina paired-end metabarcodes from raw reads through to taxonomic assignments using Snakemake; provides workflows for exact sequence variant assignment, OTU generation, and single-read processing; assigns taxonomy with the RDP classifier (naive Bayesian); trims ITS flanking rRNA regions and removes pseudogenes; uses a Conda environment for dependency management.