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Bracken

Computes the abundance of species in DNA sequences from a metagenomics sample

https://ccb.jhu.edu/software/bracken/

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                 Enterobacteriaceae

The 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