How best to pick kmer's for spades assembly?
I am wanting to de novo assemble an illinima sequences isolate at 150bp with Spades.
After QCing with bbtools my sequence length distribution has predictably changed to have a range of 10-150. Do I base my kmer choice on original read length or must I adjust for these not shorter reads.
Initially I planed to run at kmers of 55 77 99 127.
See full read length distribution here
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robert.murphy •
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Let SPAdes do the picking automatically, to being with.
Does the auto pick run at multiple kmers and then merge the assemblies? That is (as I understand it?) what manually picking specific kmers does?
Answered my own question, it does this by default so auto select seems the best.
This thread is likely of interest.
That is where I got my answer :)