No output for small bacterial genomes about smashpp

[pratas]

Dear Martin,

I am sorry for the late answer.
I think it is just a matter of optimizing the parameters.
If you want and you can share these files, I will optimize these parameters for you.

Best regards,
Diogo

[kattruels]

Hi!

I am having the same issue with E. coli genomes. Similarly, they show up in Mauve. Any suggestion of optimal segment length for a 4.5 Mb chromosome? I'll try several options... I'll report back if I find it!

[pratas]

Hi Kat,

can you please provide the IDs or sequences?
If they are private, alternatively, please try:

conda install -c bioconda smashpp -y
smashpp -v -nr -ft 0 -rm 16,0,0.1,0.95/7,0,0.1,0.95 -f 20000 -d 1 -m 500 -th 1.5 -r ECOLI_1.fa -t ECOLI_2.fa
smashpp -viz -nrr -nr -m 500 -o ECOLI_1.fa.ECOLI_2.svg ECOLI_1.fa.ECOLI_2.fa.pos

Assuming ECOLI_1.fa and ECOLI_2.fa are the sequences.
It is a matter of optimization...

Best regards,
Diogo