Classification is run in the same way as in Kraken:

kraken --db seed-kraken-db --preload --threads 20 input.fa > output.out 2> output.log

To classify seed-Kraken will use the spaced seed stored in the file seed-kraken-db/spaced_seed_sequence.

Output format

Output format differs slightly from the original Kraken. An example line in the output file:

C       A_hydrophila_HiSeq.18518        1288394 101     0:62|644:2 1288394:3 644:2 1288394:7 644:48

Notice | separating classification outputs for sense/anti-sense strand. Refer to README of the original Kraken for precise description of the output.