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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
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interpreting the image of cold #137

Closed dcopetti closed 4 years ago

dcopetti commented 4 years ago

Hi, I am using KAT to assess the completeness of a long read WGS assembly. I run KKAT comp and it looks OK: Rab1_flye191004_kat23-main mx spectra-cn_160 I know there are parts missing and others collapsed. Then I run KAT cold on the same files, and I get this: Rab1_flye191004_kat-cold How should I interpret it? Looks like there are lots of contigs at high multiplicity (orange circles). Can the cloud on top left be indicative of a contamination (e.g. endophitic fungus in a plant sample)? Thanks, Dario

gonzalogacc commented 4 years ago

Hi Dario. Please check the section 4.4 of the walkthrough, where GCP plots are described. The plots are slightly different but the idea is the same. Best Gonza.-

dcopetti commented 4 years ago

Hi @gonzalogacc ,

I wonder if you have time to address the issue #128 , where we can't run the distanalysis.py script. For me it would be very useful to select the right peaks to get better stats on my genome and assembly. Thanks! Dario