Visualization Tips

Two options you can consider when making a visualization for a genome that might make it look better: --sort_contigs and --natural_colors.

The --sort_contigs will sort by scaffold size, which tends to make the layout look nicer and more compact for draft genomes. This is not on by default because some people use order to communicate other information such as placing mitochondria at the end of the file. A major advantage to sort_contigs is the positions of all the titles. Contigs smaller than 10k will not get their own title; draft genomes can often contain >10,000 orphaned contigs that would take longer and more space to render their titles than the nucleotides themselves.

--natural_colors looks good particularly close up. If you are inspecting an individual column, you will probably find the default (255,0,0) colors too harsh and could distort your color perception. Natural colors was introduced to deal with this problem. However, any colors besides the maxed out default colors lose some contrast on large scale features while zoomed out. There's plans to have the display switch between the two color settings automatically. You could contribute with a pull request.

--base_width can be used to change from the default 100 nucleotide columns. Setting this width to a tandem repeat size, for example 171bp for centromeres, will cause them to appear as vertical lines. Base width is also useful when visualizing square table data that's not necessarily a sequence at all. Just set base_width to be your number of columns in characters and you can use FluentDNA architecture to explore any kind of big data.