Cataloging pangenomic tools

Information

With hundred of tools are labelled as ‘pangenome graph’ or ‘variation graph’ on github, it is technically impossible to have a complete and comprehensive catalog of tools.

This section will try to cover as much tools as it can, pointing to existing catalogs and more in-depth descriptions of tools when I used them.

Known catalogs or blogs:

• Catalog from the PGGB team
• awesome-pangenomes by Colin Davenport

Tools:

• bubblegun, a bubble and superbubble caller
• gfaffix, a tool to simplify graphs
• gfapy, a python library to handle GFA format
• odgi, a toolkit for pangenomes
• gfagraphs (own work) a library to handle GFA format
• pancat (own work) a small toolkit for pangenomes