Nucmer output plot


I have done some Nucmer alignment with a set of genome sequence retrieved from UCSC genome browser against my genome assembly. And the plot looks like pic above. But the contig or scalfold names are blurred just because of the limited space on X-axis. Is there any way to view or read which contig or scalfold are best maches from the plot or the alignment files?

1 Like

Hi @daikez

The option Plot Size option can be adjusted – the default is “small”, but “large” would be better given the number of sequences. There are other plot variables that you can adjust if needed (example: Plot a particular reference or query sequence?).

You can also hide the tool and history panel in the Galaxy application to give the plot more space, or open your browser window larger, or download the plot and open it that way.

Hope that helps!

Thanks for the tips!

I have tried the large sized plot. Though it’s better, it’s still not possible to see the names of the matched contigs or scaffolds. I have tried to adjust X and Y axis value with no success. I have also run the querry sequences against the RepeatMasked assembly and it has returned much better and clearer plot.

Finally, I have tried “Delta-filter” on the alignment generated with Nucmer, and it showed the best matched contigs and scaffolds. And I think it’s good enough for me.