Is MEGAHIT assembly output supported?

[chengwbTOT]

Hello,

Thanks for developing PlasMAAG. I am interested in applying it to my metagenomic datasets.

I noticed that the documentation/paper mainly discusses assembly graphs from SPAdes (e.g., assembly_graph.fastg or .gfa). My assemblies were generated using MEGAHIT, which produces a final.gfa file.

Could you please clarify:

Does PlasMAAG support the GFA format output by MEGAHIT directly?

Are there any specific parameters or preprocessing steps required when using MEGAHIT graphs instead of SPAdes graphs?

Thank you for your help!

[Las02]

Hi @chengwbTOT,

At the moment, PlasMAAG only supports SPAdes. However, since there seems to be interest in running PlasMAAG on MEGAHIT output (eg. see #7), I think it would be worth looking into supporting this as well.

What are your thoughts, @Paupiera?

Best,
Lasse

[Paupiera]

Hi @chengwbTOT,

Thanks for considering PlasMAAG as your tool. We are indeed considering updating PlasMAAG so it also works on MEGAHIT assemblies. We will update the repository as soon as we have some news about it.

Thanks,
Pau