plot_nucmer¶

Plot_nucmer is a simple conda package that aims on rapidly and easily running an alignment with nucmer and visualising its results.

Installation¶

Installation is described in the github main page.

Conda package¶

> Users are advised to create separate conda environments

# Get the conda package
mamba create -n plot_nucmer -c conda-forge -c bioconda -c falmeida plot_nucmer

Tip

Users are advised to use mamba since it is faster.

Docker image¶

# pull and enter the image
docker run --platform linux/amd64 -v $(pwd):/work -w /work -it fmalmeida/plot_nucmer

# run the script from inside the container
root@c896e9370a2f:/work# plot_nucmer --help

Available features¶

This script is designed to:

Perform whole genome alignment between FASTAs with nucmer.
Filter alignments by length and identity
Plot these alignments in circular visualisation with ggbio.

It is an automation of the methods described by Taylor Reiter at https://taylorreiter.github.io/2019-05-11-Visualizing-NUCmer-Output/.

Support Contact¶

Whenever a doubt arise feel free to contact me at almeidafmarques@gmail.com