Skip to content

Latest commit

 

History

History
75 lines (46 loc) · 4.88 KB

README.md

File metadata and controls

75 lines (46 loc) · 4.88 KB

Panache: PANgenome Analyzer with CHromosomal Exploration

Panache is a web-based interface designed for the visualization of linearized pangenomes. It can be used to show presence/absence information of pangenomic blocks of sequence or genes in a browser-like display.

Snapshot of banana data in Panache

Live demo

An instance of Panache is currently running at https://panache.ird.fr/ where anyone can upload its own data.

To see an instance with an existing dataset (Banana Pangenome by Rijzaani H. et al, 2021), you can visit the Banana Genome Hub.

Citation

Éloi Durant, François Sabot, Matthieu Conte, Mathieu Rouard, Panache: a web browser-based viewer for linearized pangenomes, Bioinformatics, Volume 37, Issue 23, 1 December 2021, Pages 4556–4558, https://doi.org/10.1093/bioinformatics/btab688

Installation

With Docker

Panache comes with a Docker container. Please make sure your machine already have Docker and Docker-compose (version >= 1.10) installed. If not, you might install it using apt install docker docker-compose.

!CAUTION! Somehow the installation does not work with the "bullseye" distribution of debian, to correct related bugs you can modify the Dockerfile and in the first line replace FROM debian with FROM debian:buster. Then proceed as follows:

After cloning Panache's repository, the container can be built and launched running bash start.sh (with your sudo rights enabled; this will both create a build version and serve it with nginx).

The web interface will be available after 4-ish minutes once everything is built. If you are impatient and want to see what is happening live, you can also run the same command that is in start.sh without the -d option, which hides the standard output from the generated container. Access the visualization through your localhost (by default a dev version will be served throught port 8080 and a prod version through port 1337).

The visualization could be served on a custom IP when specified inside the nginx.conf file, instead of (or alongside with) localhost.

Without Docker

If you wish to use another web server directly with the production version of files instead, you will have to run npm install, followed with npm install @vue/cli. Finally make sure to run npm run build to have the production version files available, they will be all stored in the directory called 'dist', ready to be served.

Main features and documentation

Animated GIF introducing the main features of Panache

Panache offers an interactive view of a presence/absence matrix of genomes and 'pangenome blocks'---such blocks being either sequences or gene. This matrix can be explored similarly to genome browsers, by clicking on the desired location on the miniature.

More descriptive documentation (FAQ, feature description, linearization...) is available at Panache's wiki.

Representation

Panache was built to display linear representations of pangenomes instead of graph-like display. With every block ordered on a single string, it becomes easier to parse the representation with human eyes and makes sense of per-node data. It also makes a good baseline for additional information or metadata, that can be layed out on dedicated spaces without overloading the rest of the visualization.

Visual explanation of pangenome linearization

Data inputs

File examples can be find in the public folder, and detailed information are available in the Files and Formats section of the wiki

Full Documentation

See the Wiki for full documentation, examples and other information.

Acknowledgement

Panache would not have come to light without the help of Romain Basset (transition to Vue JS framework), Mel Florance (Docker container and various enhancements) and Alexandre Bousquet (Various improvements and Sorting options for the genomes). Thank you to Gaetan Droc for setting up Panache on the Banana Genome Hub and Philipp Bayer for his hard-won version of wheat_panache.

License

Panache is published under the terms of the MIT LICENSE

Contact

Eloi Durant or Mathieu Rouard


Miscellaneous

panache, noun

  1. an ornamental tuft (as of feathers) especially on a helmet
    The palace guard had a panache on his helmet.

  2. dash or flamboyance in style and action
    flashed his … smile and waved with the panache of a big-city mayor. — Joe Morgenstern

Definition from Merriam-Webster