Metagenomics nanopore data

Question

[Sitara]

Hello all

I have downloaded public nanopore metagenomic data. I have used minimap2 for the alignment of long nanopore reads. I am interested in calculating the abundance for each organism. Can someone suggest any tool to get the abundance from nanopore reads?

Any help would be appreciated. Thanks in advance.

[WouterDeCoster]

I have used minimap2 for the alignment of long nanopore reads.

Aligned to what?

[Sitara]

Aligned to NCBI bacterial reference sequences