Can GraphBin be used with a co-binning approach? about graphbin

[Vini2]

Hello @Laura-Alex,

Thanks for your interest in GraphBin.

There can be cases where the same contig identifier appears in two or more samples. So you should rename the contigs in the contig file to be sample-specific. For the assembly graphs, first, you can convert the individual FASTG files to GFA and rename the contig identifiers to be sample-specific as well. Then you can concatenate the contig files separately to make one FASTA file and the graph files separately to make one GFA file.

I guess this should work fine but I'm not sure until I test it. I will test this and get back to you ASAP.

Thanks for your question!

Best regards,
Vijini

[Vini2]

Hello @Laura-Alex,

I think you can use an assembler such as Flye and do a population assembly using the contigs from all the MEGAHIT assemblies and get a non-redundant set of contigs. This sort of assembly is done in Hecatomb tool. Then you can run the Flye version of GraphBin on the resulting contigs and Flye assembly graph.

Hope this helps.

Best regards,
Vijini