Bracken¶
Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Bracken uses the taxonomy labels assigned by Kraken, a highly accurate metagenomics classification algorithm, to estimate the number of reads originating from each species present in a sample.
Profile Format¶
The following input format is accepted by taxpasta
. This file is generated with the Bracken parameter -o
. A tab-separated file with the following column headers:
Column Header | Description |
---|---|
name | |
taxonomy_id | |
taxonomy_lvl | |
kraken_assigned_reads | |
added_reads | |
new_est_reads1 | |
fraction_total_reads |
Example¶
name taxonomy_id taxonomy_lvl kraken_assigned_reads added_reads new_est_reads fraction_total_reads
Homo sapiens 9606 S 156 0 156 0.90173
Saccharomyces cerevisiae 4932 S 17 0 17 0.09827
-
Value used in standardised profile output ↩