A short background: I have 4 metagenomes. In all of them, two very closely-related populations of the same bacterial cluster co-occur. I obtained 4 final bins, and according to ANI value, I have two different genomes (ANI around 80).
The point is, when I extract the rRNA genes from the bin (assembled with SPAdes), the rRNA looks identical. Which is not possible - the only explanation I came with is that SPAdes is not able to resolve the 16S, so it will assemble just one instead of two. Roughly speaking, it 'mixes' the reads from the original rRNAs and it ends up with just one sequence.
Is it any tool that would allow me to extract the two different rRNAs? I had a look into reago (edited) but it looks like it is not updated anymore, and there are some parameters to set which are not clear (e.g., -l for the length of the input reads, which is supposed to be uniform).
Thanks all and have a nice weekend!