sunnycqcn / 2020-stacked-dot-plots

Stacked dot plots

an exploratory repository

Run mashmap or nucmer to find alignments between a query genome and one or more target genomes; plot, dot-plot style.

See the source in alignplot.py and the dotplot notebook for more info.

The first two examples below are of "non-stacked" dotplots, as in, they are just pairwise dotplots.

The third example below "stacks" the dotplots on the x axis, so that you can see two dotplots against the same query genome in the query genome coordinates, but with the target genomes split out.

installation and running

For now, if you want to try this out for yourself --

• you'll need python3 installed
• you'll need mummer4 and/or mashmap installed, along with matplotlib.
• you'll need to put genomes somewhere (e.g. the genomes/ directory)
• you can add names or replace names in info.csv
• see the source in alignplot.py and the dotplot notebook for more info on actually running.

(More work to be done here -- will binderize eventually :)

examples

Shared sequences (contamination?) between two Genbank genomes.

Here, the Rokubacterium (red, x axis) is probably contaminated by sequences from the Acidobacterium (y axis coordinates).

Shared sequences between a TARA MAG and a Genbank genome.

The TARA binned genome/MAG is on the y axis, the Genbank genome is on x in red.

Shared sequences between a TARA MAG and two Genbank genomes.

The TARA binned genome/MAG is on the y axis, the first Genbank genome is on x in red, the second is on x in blue.

contact

Titus Brown, [email protected]

CTB Nov 2020