BCdatabaser

BCdatabaser creates marker- and taxon-specific reference sequence databases from NCBI data for DNA barcoding and meta-barcoding and prepares them for taxonomic classifier training.

Key Features:

• Customizable Database Creation: Generates reference databases for arbitrary genetic markers and taxonomic groups using NCBI sequence records.
• Optional Sequence Processing: Supports optional sequence trimming and orientation during database construction.
• Data Filtering and Formatting: Applies user-specified filtering and formats output for (meta-)barcoding requirements.
• Taxonomic Classifier Training: Produces datasets prepared for training taxonomic classifiers for sequence-based identification.
• DOI Assignment: Enables assignment of a Digital Object Identifier (DOI) to generated databases for citation and metadata tracking.

Scientific Applications:

• DNA barcoding: Produces reference sets for marker-based species identification in single-specimen barcoding studies.
• Meta-barcoding: Prepares formatted reference databases for taxonomic assignment in mixed-sample meta-barcoding analyses.
• Cross-domain taxonomic studies: Applicable to microbiology, plants, and animals for taxon-level identification across diverse biological contexts.

Methodology:

Integrates NCBI sequence data with user-defined parameters to construct reference databases, including optional sequence trimming and orientation, user-specified filtering and formatting for (meta-)barcoding, and support for training taxonomic classifiers.