README.md

# Pan1c_View


## Name
Pan1c_View

## Description
Report builder for [Pan1c](https://forgemia.inra.fr/alexis.mergez/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
Follow [this link](https://web-genobioinfo.toulouse.inrae.fr/~bardou/pan1c_qc/?id=11Ch-v1b) to see a sample Pan1c View report.

## 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_qc.git`

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

Access the report on your webserver : `https://mywebserver.fr/pan1c_qc/?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
Show your appreciation to those who have contributed to the project.

## License
Pan1c View source code is distributed under the GPL3 license.