MarkerScan

MarkerScan identifies and assembles high-quality genomes of non-target organisms (cobionts) co-sequenced with target species to detect and mitigate contamination and mislabeling in eukaryotic genome sequencing projects.

Key Features:

• Cobiont detection and assembly: Detects and assembles high-quality genomes of non-target organisms (cobionts) co-sequenced with target species.
• Taxonomic profiling of assemblies: Performs taxonomic profiling on assemblies derived from raw sequencing data.
• rRNA marker identification: Identifies small ribosomal RNA (rRNA) sequences within assemblies to serve as taxonomic markers.
• Targeted classification and retrieval: Uses a targeted classification strategy based on rRNA markers to retrieve and assemble high-quality cobiont genomes.
• Contamination detection and mitigation: Identifies and facilitates removal of non-target genomes from target species assemblies to mitigate contamination.
• Mislabeling detection: Detects potential mislabeling in public genomic databases by identifying unexpected taxonomic assignments.
• Pre-submission checks: Supports pre-submission checks to identify obvious contaminations prior to database submission.

Scientific Applications:

• Biodiversity genomics: Improves accuracy of biodiversity genomics by recovering cobiont genomes from mixed-species samples.
• Database curation: Prevents propagation of erroneous taxonomic relationships in public genomic databases by detecting contamination and mislabeling.
• Discovery of endosymbionts and environmental organisms: Enables discovery of endosymbionts and environmental organisms present in sequencing samples through targeted cobiont assembly.
• Support for further scientific inquiry: Provides cobiont genomes for further investigation of biological interactions and phenomena within ecosystems.
• Pre-submission quality control: Supports quality-control workflows to reduce contaminated entries in public repositories.

Methodology:

Performs taxonomic profiling of an assembly derived from raw sequencing data, identifies small ribosomal RNA (rRNA) sequences as markers, and applies a targeted classification strategy to retrieve and assemble high-quality cobiont genomes.