Lite Kraken/Bracken Databases Built Using UHGG Genomes

Two Kraken/Bracken databases built from the Unified Human Gastrointestinal Genome (UHGG) collection. The HUMAN_3006 database contains 3,006 high-quality species clusters, each represented by a single genome. The UHGG_5987_KRAKEN database represents the same clusters using 5,987 genomes selected to maximize taxonomic diversity. These databases were created by Benjamin S. Beresford-Jones at the University of Cambridge using Kraken v2.1.2 and Bracken v2.6.2.

Use Cases

• Classify metagenomic sequencing reads based on the UHGG reference genomes.
• Estimate species abundance in microbiome samples using the Bracken algorithm.
• Benchmark taxonomic classification tools against a standardized, high-quality genome database.

Strengths

• Built from the high-quality, curated UHGG genome collection.
• Provides two distinct database versions with 3,006 and 5,987 genome entries for flexibility.
• Includes the specific commands used for database construction, ensuring reproducibility.

Limitations

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

Provenance

Source

University of Cambridge

Collection Method

Databases built from the Unified Human Gastrointestinal Genome (UHGG) collection using Kraken v2.1.2 and Bracken v2.6.2.