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.
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.
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
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.
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.
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.
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.
File examples can be find in the public folder, and detailed information are available in the Files and Formats section of the wiki
See the Wiki for full documentation, examples and other information.
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.
Panache is published under the terms of the MIT LICENSE
Eloi Durant or Mathieu Rouard
panache, noun
an ornamental tuft (as of feathers) especially on a helmet
The palace guard had a panache on his helmet.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