Bracken

Bracken re-estimates taxonomic abundances from Kraken 1, KrakenUniq, or Kraken 2 classification output to provide accurate species- and genus-level abundance profiles from shotgun high-throughput DNA sequencing reads.

Key Features:

• Kraken integration: Uses read-level classifications produced by Kraken 1, KrakenUniq, or Kraken 2 as the input basis for abundance estimation.
• Bayesian re-estimation: Applies a Bayesian approach to reassign and redistribute reads from Kraken assignments to compute taxon abundances.
• Genomic adjustment: Incorporates genomic information to correct for biases in read distribution across different taxa.
• Taxonomic resolution: Produces abundance estimates at multiple hierarchical levels, explicitly including species and genus.
• Input data: Operates on raw shotgun metagenomic high-throughput DNA sequencing reads.
• Complex-sample sensitivity: Capable of producing reliable abundance estimates in samples containing multiple near-identical species.

Scientific Applications:

• Microbial community profiling: Quantifies organismal composition of environmental or host-associated microbiomes using shotgun sequencing data.
• Fine-resolution abundance estimation: Provides species- and genus-level abundance profiles beyond marker-gene surveys such as 16S ribosomal RNA gene sequencing.
• Population structure analysis: Facilitates comparative analyses of microbial population structure and dynamics across samples.

Methodology:

Bracken uses Kraken classifications as the foundation and applies a Bayesian re-estimation procedure that incorporates genomic information to adjust read distribution and compute taxon abundances.