Build KI-S singularity container :

sudo singularity build ki-s.sif ki-s_from_ubuntu.def

Let's start by assessing relatedness between your favorite genome (MyGenome) and genomes available in public databases. Example directory contains 14 fasta files of genomes in zip archive 14gx.zip :

cd ki-s/example

Calculation of the percentage of shared 15-mers between all genomes

singularity run ../ki-s.sif /usr/local/src/ki-s/ki-s.pl -z gx14.zip -m kmers -k 15 -o gx14k15s

Generate circle packing representation of this matrix (informations to color points are in gx14_infos.tab file ) :

singularity run ../ki-s.sif /usr/local/src/ki-s/tools/generate_packing.pl -in gx14k15s_matrix_kmers.csv -car gx14_infos.tab -o=gx14k15s_circ -thrs="'0.5;0.8;0.9'"

Open gx14k15_circ/gx14k15_circ.html with a web browser, you can see your favorite genome (MyGenome) is a Xylella fastidiosa subsp. pauca strain.

You can also compute ANIb (even if it is more time-consuming) :

singularity run ../ki-s.sif /usr/local/src/ki-s/ki-s.pl -z gx14.zip -m ani -bl=ANIb -o gx14anibs

And create circle packing representation of this matrix :

singularity run ../ki-s.sif /usr/local/src/ki-s/tools/generate_packing.pl -in gx14anibs_matrix_ani.csv -car gx14_infos.tab -o=gx14anibs_circ -thrs="'0.95;0.98;0.99'"
  

Open gx14anib_circ/ gx14anib_circ.html with a web browser, ANIb confirm that MyGenome is a Xylella fastidiosa subsp. pauca strain.