When working with Jellyfish, I used sample command in their guide:
$ jellyfish count -m 22 -s 100M -t 16 -C merged.fq.gz
and I am not really understand the meaning of -C, which is described as "canonical", or (as in Jellyfish 1) "Count both strand, canonical representation". Doesn't it should be a default option (no need to put in)? What is the consequence if I do not include this -C in my jellyfish command?
I also wonder that is this option also pre-implemented in kmergenie?
Thank you in advance for your clarification!