Converting GFA to rGFA

Question

[Ric]

Hi, Are there any tools that convert GFA to rGFA?

Answer 1

[colindaven]

No - they are fundamentally different approaches, and GFA is far more popular.

• GFA is used by many tools (minigraph-cactus, PGGB etc)
• reference GFA rGFA is used by a more limited set of tools around Heng Li's minigraph. The entire reference genome is the first part of the rGFA format which is very different to GFA.

See the in depth blog post here: https://ekg.github.io/2019/07/09/Untangling-graphical-pangenomics

Here is a list of links on the different tools and formats:

https://github.com/colindaven/awesome-pangenomes

[guntul]

In gfatools, it says rgfa is a subset of gfa. So, is it then possible to convert rgfa to gfa?

[Ric]

I used nf-core/pangenome which created a GFA file. We found panGraphViewer in order to visualize nf-core/pangenome GFA file. However panGraphViewer requires a rGFA. However, it supposed to be able to convert GFA to rGFA but in my case it failed to do it.

I looked into gfatools but did not understand how to use it.

[m.t.lorenc]

PanGraphViewer failed to convert nf-core/pangenome GFA to rGFA file? What could be the reason?

[Ric]

I failed with gfa2rGFA.py too.