META-GECKO

META-GECKO performs post-processing of metagenomic taxonomic classifications to refine taxonomic mapping, detect low-abundance bacteria, and filter spurious matches for improved interpretation of uncultured genomes in environmental and fecal microbial community sequencing data.

Key Features:

• Enhanced Taxonomic Mapping: Improves identification of differences in read abundance assigned to taxa and refines read-to-taxon mapping.
• Detection of Low-Abundance Species: Detects reads from low-abundance bacteria to provide evidence for rare species presence.
• Spurious Match Filtering: Filters spurious sequence matches to reduce false-positive taxonomic assignments.
• Innovative Visualization Techniques: Provides visualization approaches to display metagenomic diversity and read-to-taxon mappings.
• Flexible Reference Database Utilization: Enables the mapping process to be conducted using various reference databases.
• Extensible Platform for Plugin Development: Specifies datafile formats and mapping processes to facilitate development of plugins for additional post-processing.

Scientific Applications:

• Species Identification and Abundance Tracking: Identifies species present in environmental samples and tracks changes in their abundance across conditions.
• Fecal Microbiome Analysis in Twin Studies: Applied to analyze fecal microbial communities of adult female monozygotic and dizygotic twin pairs concordant for leanness or obesity and their mothers.

Methodology:

Post-processing of taxonomic classifications; mapping reads to taxa using specified mapping processes and reference databases; detection of low-abundance bacterial reads; filtering of spurious matches; generation of visualization outputs; use of specified datafile formats and plugin-enabled post-processing.