User Guide

Squiggle is designed to be easy to use while still providing complete flexibility to the user. For the sake of demonstration, we’ll be using four different species’ β-globin genes (human, chimpanzee, rhesus macaque, and Norway rat).

For a full list of the command line options and their meanings, see the CLI Reference.

Basic Usage

The easiest way to visualize a sequence is by passing a FASTA file to Squiggle:

$ squiggle human_HBB.fasta
Bokeh Application

To use a different visualization method, provide --method with a setting (see Visualization Methods for a description of the supported methods):

$ squiggle human_HBB.fasta --method=gates
Bokeh Application

Plotting Multiple Sequences

If your FASTA file has multiple sequences, they will get plotted together automatically. If, however, your sequences are in separate files, you can still plot them together by passing multiple files to Squiggle:

$ squiggle human_HBB.fasta chimpanzee_HBB.fasta norway_rat_HBB.fasta rhesus_HBB.fasta
Bokeh Application

To put them on separate plots, use the --separate flag:

$ squiggle human_HBB.fasta chimpanzee_HBB.fasta --separate
Bokeh Application

By default, their \(x\) axes are linked. This can be disabled with --no-link-x (try if for yourself by panning around):

$ squiggle human_HBB.fasta chimpanzee_HBB.fasta --separate --no-link-x
Bokeh Application

Similarly, the \(y\) axes can be linked and unlinked with --link-y/--no-link-y.

Note that when plotting seperately, Squiggle will try to make the layout as square as possible. If you want to specify the number of columns, you can do so with the -c option.

If you want to compare FASTA files, you can use the --mode=file flag to treat each file as a separate entity, as opposed to each sequence. The --mode=auto flag (which is the default) will attempt to visualize each sequence independently unless there are too many, in which case it will switch to file mode.

As an example, let’s compare the highly expressed genes of E. coli and B. anthracis. Because there are so many sequences, we are going to downsample them by a factor of 25 using the -s flag in order to improve performance:

$ squiggle ecol.heg.fasta banth1.heg.fasta -s 25
Bokeh Application