LULU

LULU curates operational taxonomic unit (OTU) tables from metabarcoding datasets by merging likely erroneous OTUs based on sequence similarity and co-occurrence patterns to improve biodiversity metrics.

Key Features:

• Error Reduction in OTU Tables: Identifies and merges low-abundance OTUs into more abundant parent OTUs using co-occurrence patterns and user-defined criteria to reduce erroneous OTUs.
• Integration with DADA2: Operates downstream of Illumina read correction and ASV inference performed with DADA2.
• Clustering and Curation with swarm v2: Works in conjunction with swarm v2 to cluster Amplicon Sequence Variants (ASVs) into OTUs and further curate clusters based on sequence similarity and co-occurrence.
• Taxonomic Assignment Support: Compatible with taxonomic assignment using the RDP Bayesian classifier and BLAST.
• Multi-marker Compatibility: Applicable to prokaryotic 16S and eukaryotic markers 18S and COI.
• Alpha Diversity Refinement: Curates ASVs into OTUs to produce alpha diversity estimates more consistent with the biological species concept, with performance influenced by identity-threshold settings (notably in 18S data).
• Validation Evidence: Validated on eukaryotic mock communities and deep-sea sediment samples showing improved reliability of biodiversity inventories.

Scientific Applications:

• Environmental Metabarcoding: Refining OTU tables for biodiversity assessments in marine and terrestrial biomes.
• Metazoan Biodiversity Inventories: Producing more reliable metazoan inventories from ASV/OTU data.
• Comparative Diversity Metrics: Improving alpha diversity estimation for ecological research and conservation studies.
• Multi-domain Marker Studies: Supporting analyses across 16S, 18S, and COI marker-based studies.

Methodology:

Illumina read correction and ASV inference using DADA2; clustering ASVs into OTUs with swarm v2; applying the LULU algorithm to refine clusters based on sequence similarity and co-occurrence patterns; taxonomic assignment via the RDP Bayesian classifier and BLAST.