Hello,

I need to extract kmers and their counts per contig in an assembly file and I was wondering what would be the most efficient way to do this?

For previous full genome kmer counts I've used BBTools kmercountexact.sh and I have considered ways to fed each scaffold into that program, but I have two issues with that potential solution. The first is the sheer number of output files that would result from doing that, although I guess I could just cat them all at the end. The second is I am very unfamiliar with awk/ bioawk and so while I know bioawk allows you to extract sequences very easily I don't know how to set up a for loop using awk/bioawk to do this and then pipe the contigs into another program.

Would anyone be kind enough to help me with this or direct me to a more appropriate solution?

Thank you!