Short Reads assembly at strains level for metagenomic data

Question

[steven.blanchard92]

Hello,

I want to assemble an ecosystem with several strains of the same species, but the standard assembly tools (MegaHit, spades...) don't allow me to discriminate the close strains correctly. The genome consensus results correspond to the majority strain and not to all strains.

Do you know a software to perform an assembly of this complex ecoystem but for illumina short reads only ?

I have found software like Straineberry or OPERA-MS that does this through an assembly step and mapping step , but they are only available for long reads.

Thanks,

Steven