Bracken
Supported Tool
is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample
Description
This module works with Bracken output files that resemble Kraken reports. They look like the following:
100.00 1188381 0 R 1 root
100.00 1188380 0 R1 131567 cellular organisms
100.00 1188328 0 D 2 Bacteria
99.99 1188317 0 P 1224 Proteobacteria
99.99 1188308 0 C 1236 Gammaproteobacteria
99.99 1188285 0 O 91347 Enterobacterales
99.98 1188147 0 F 543 EnterobacteriaceaeThe main assumption to tell Bracken reports from Kraken is that the former don’t have an “unassigned” category at the head of the file, and instead start with “root”.
A bar graph is generated identical to that of Kraken.
File search patterns
bracken:
contents_re: ^(\d{1,3}\.\d{1,2})\t(\d+)\t(\d+)\t((\d+)\t(\d+)\t)?([URDKPCOFGS-]\d{0,2})\t(\d+)(\s+)root
num_lines: 1