Databases for MyCodentifier: A tool for routine identification of nontuberculous mycobacte

Databases for the MyCodentifier pipeline, a bioinformatics tool for identifying Mycobacterium tuberculosis complex and Nontuberculous mycobacteria species from sequencing data. The collection includes seven major mycobacterial reference genomes, a Centrifuge classification database, and an hsp65 gene database. It was developed by researchers at Radboud University Nijmegen.

Use Cases

• Identify Mycobacterium tuberculosis complex and Nontuberculous mycobacteria species based on shotgun metagenomic data from MGIT cultures.
• Predict genotype resistance for mycobacterial species using reference-based mapping databases.
• Classify mycobacterial strains at the genome level using the Centrifuge database built from the Tortoli et al. 2017 strain collection.
• Perform fast identification of mycobacteria using the hsp65 gene KMA database.

Strengths

• Includes seven major mycobacterial reference genomes with annotation and Genbank files.
• Contains a specialized Centrifuge database built from the Tortoli et al. 2017 Mycobacterium strain collection.
• Provides an hsp65 gene database for rapid preliminary identification.

Limitations

• Row count and file size are unknown, which may limit suitability assessment.
• Column-level documentation is absent; field semantics must be inferred after download.
• Last update date is unknown; freshness unverified.

Provenance

Source

Radboud University Nijmegen

Collection Method

Compiled as reference databases for the MyCodentifier bioinformatics pipeline.