simple python script that takes Bracken outputs and merges them into one OTU table, user can specify if a subset of outputs need to be summed together prior to appending to the OTU table
Bracken2OTU.py -i *.bracken -sum sum_by_lane -o merged.otu
where sum_by_lane is a two field (tsv) textfile where each line stipulates in the first field the name of the summed OTU entry and the second field, a "+" delimited list of the bracken filenames that should be summed to make said entry