How to set kmer value of spades in ARC config file?

[samhunter]

Currently this option isn't supported, however I have been considering the idea of adding a parameter which would allow the user to override all assembly settings.

In the mean time, if you want to add modified k-mer settings manually you could do it easily in by modifying one line of the code. (I haven't tested this, but I believe it should work fine).

In "assembler.py" look for line 218 which should say: args = ['spades.py', '-t', '1']

Change this to something like: args = ['spades.py', '-t', '1','-k','15,25,35']

Where '15,25,35' are the kmer sizes you want.

Sam

[quxiaojian]

Thanks Sam. I will have a try. Before this editing, I have to modify kmer_short in script of spades. Hope this setting be valid. Thanks for your quick response. XJ