K-mer sequence of k-mer with specific frequency

TGAC / KAT

The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.

http://www.earlham.ac.uk/kat-tools

GNU General Public License v3.0

200 stars 51 forks source link

K-mer sequence of k-mer with specific frequency #149

Closed dbau-igenomix closed 2 years ago

dbau-igenomix commented 3 years ago

Hi,

Is it possible to get the k-mer sequence associated with each k-mer frequency obtained with kat hist? For example:

# Title:9-mer spectra for: phiX.fasta
# XLabel:9-mer frequency
# YLabel:# distinct 9-mers
# Kmer value:9
# Input 1:phiX.fasta
###
1 4972
2 189
3 8
4 1
5 0
6 0
7 0
8 0
9 0
...

Would it be possible to the the sequence corresponding to the 9-mer with frequency 4?

Thanks, Davide

bjclavijo commented 2 years ago

Hi Davide. I'm sure you've already sorted this one out, but in case you have not, jellyfish has that functionality.