How to choose kmer length?

dzerbino / velvet

Short read de novo assembler using de Bruijn graphs, as published in: D.R. Zerbino and E. Birney. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research, 18: 821-829

https://europepmc.org/article/pmc/2336801

GNU General Public License v2.0

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How to choose kmer length? #48

Closed XMTian closed 3 years ago

XMTian commented 3 years ago

Hello,

I'm using velvet to assemble genomes, but I don't know how to choose kmer length. I tried to use velvetoptimiser, but I failed in the installation. So can you tell me how to choose by myself?

Thanks a lot.

dzerbino commented 3 years ago

Dear @XMTian ,

Please refer to our short summary here: https://www.ebi.ac.uk/~zerbino/velvet/hash_length_choice.html

Or a longer explanation here: https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471250953.bi1105s31

Best regards,

Daniel