Soapdenovo Multi-Kmer (-M) Option

Question

[snek]

Hi all,

Can anyone give a sample command for using multi-kmer option (-m) in SOAPdenovo2? At which steps should we use this option? It is mentioned somewhere in the literature that this kind of multi-kmer assembly is used in the contig step, then do we use it in sparse-pregraph step or not? And if we don't use -m in sparse-pregraph step, what -K parameter should be given?

Thank you and regards, Snehal

Answer 1

[Xingyu Yang]

You can just use this option in "all". Or use it in the "contig" step. No need to use it in sparse_graph step. In sparse_graph step, use another fixed kmer size.

[snek]

Thanks I will try as per your suggestion.