is there a way to get the kmer counts of the kmers in the produced unitigs?

[shokrof]

Hi,
I am wondering if I can get the kmer counts along with the unitigs fasta files.

Thanks,
Moustafa

[jamshed]

Hello Moustafa,

We do not support this at this moment, unfortunately. It might be doable, given that we have the corresponding KMC databases; but attaching the k-mer counts to the unitigs is non-trivial in cuttlefish.

[shokrof]

is there a way to keep the KMC databases? I can make an easy script to get the kmer counts if can get the kc databases

[jamshed]

Hi @shokrof: are you using cuttlefish 2, i.e. using the --read or --ref arguments? If yes, then we have valid counts only for the (k + 1)-mers—the k-mers are extracted from them and their counts aren't obtainable in a straightforward manner from the (k + 1)-mers. If the (k + 1)-mer counts would do, then I can post some instructions here to retain the KMC databases.

[rchikhi]

Here's what to change to retain the KMC database of (k+1)-mer counts:
keep-edges-counts-diff.txt