Strategy for using MetaCoAG with Hybrid Assembly Contigs

[sixvable]

Hi guys.

Thanks for creating such a good binning tool.

I was wondering which kind of strategy should I choose if I am going to bin the hybrid assembly from hybrid metagenomic assembly tools such as hybridSPAdes or Flye + short reads post-polishing ?

Due to the budget limitation, we only have 10GB ONT reads + 30 GB illumina PE150 reads for one sample. Currently we choice two hybrid assembly strategy:

1. Directly hybrid assembling using metaspades with --ont
2. Assembling just ONT reads with metaflye and polishing the contigs with illumina reads using Polypolish --careful

Is it still appropriate to bin those two results with MetaCoAG? Is there any tips for such case?

sixvable

[Vini2]

Hi @sixvable,

Thanks for your interest in MetaCoAG.

You can bin both those results using MetaCoAG. You can use the relevant spades and flye assembler options in MetaCoAG.