Reliably detect M.bovis when it's at low prevalence in the sample

[ellisrichardj]

Need to filter kraken/bracken output so that presence of M.bovis in the sample is recognised and flagged. This should be added to the output csv file

[ellisrichardj]

M. bovis is classified as 'S1' level in kraken output (M. tuberculosis var. bovis) so bracken needs to filter on this level

[ellisrichardj]

Use grep to parse bracken output for M.bovis presence. However, if not present grep gives and exit code and process fails.

[ellisrichardj]

Need to look though existing data and determine threshold / cut-off abundance for positive/negative