Classification
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.