Coverage of Synteny

[ideshigenomics]

Hello
I have Bacterial a 5.4 mbp draft genome of Bacteria with 64 contigs. However, the synteny blocks only covers a small portion (first two contigs) of gemome, even for the copy-paste genomes with two different names. Please let me know if the following codes are ok-

ntSynt -d 5 Sample_1.fna Sample_One.fna

ntsynt_viz.py --blocks ntSynt.k24.w1000.synteny_blocks.tsv --fais Sample_1.fna.fai Sample_One.fna.fai --scale 50e5

Not moving to the 3rd contig, even for identical sequences.

[warrenlr]

I am glad to see that the framework is generally working at plotting, in your hands. Now the question is:
1-Is the output of ntSynt missing information from your original input?
or
2-Is ntSynt-viz not plotting all of the synteny block reported by ntSynt?

Without seeing your output, it is not possible for me to help troubleshoot, but I suspect a formatting error -- please ensure you follow the demo provided with the tool and ensure that you adhere to the provided guidelines with your data.

Perhaps you could start andswering these 2 questions (above), first looking at the output of ntSynt and making sure it is complete in respect to the original genome sequence provided. This will help us narrow it down to the actual issue and where we should concentrate our energy

Thank you for your interest in ntSynt and ntSynt-viz.
Rene

[lcoombe]

Hi @ideshigenomics,

Just to add to Rene’s response - there are default minimums for the synteny block length (--length) and the contig length (--seq_length) that will be plotted, which you may need to lower given the small size of your genome and thus the contigs, presumably. More info about all the options you can specify are here: https://github.com/bcgsc/ntSynt-viz?tab=readme-ov-file#usage-