Pan1c_View

Name

Pan1c_View

Description

Report builder for Pan1c.

Pan1c (Pangenome at Chromosome Scale) is a Snakemake workflow designed to simplify the construction and quality assessment of pangenome graphs. The workflow consists of splitting the overall graph construction into chromosome-level graph construction, followed by concatenation. This reduces the complexity of graph construction and exploration while enabling the use of cluster infrastructures, ultimately reducing the overall construction time.

Demo

Coming soon...

Installation

Production

No installation required.

All you need to do is download the code from your web server and add the data from Pan1c to the 'project' folder.

git clone git@forgemia.inra.fr:philippe.bardou/pan1c_view.git

The project folder tree:

project/        <= put Pan1c output in a "project" directory
└── 11Ch-v1b
    ├── data
    ├── Pan1c.11Ch-v1b.assembly.json
    ├── Pan1c.11Ch-v1b.graph.json
    ├── Pan1c.11Ch-v1b.tags.json
    ├── Pan1c.11Ch-v1b.var.json
    └── Pan1c.documentation.json

Access the report on your webserver : https://mywebserver.fr/pan1c_view/?id=projectid

Replace :

• mywebserver with the name of your web server
• projectid with one of the directories in the project directories.

Development

For development, a local lightweight HTTP server can be used to serve the pages (http://127.0.0.1:8080/):

npx http-server .

Authors and acknowledgment

• Philippe Bardou (philippe.bardou@inrae.fr)
• Alexis Mergez
• Christophe Klopp

We are grateful to the genotoul bioinformatics platform Toulouse Occitanie (Bioinfo Genotoul, https://doi.org/10.15454/1.5572369328961167E12) for providing help, computing and storage resources.

License

Pan1c View source code is distributed under the GPL3 license.