I am working with someone who has a set of assembled metagenomic data. These data have been assembled into 43 bins. I want to extract the potential 16S rRNA sequences from each bin to try to see if there are any potentially unique genera within these metagenomes. For each bin, I converted the BAM file to a FASTQ file and ran SortMeRNA using the bacterial 16S index as the searching database. This created FASTQ files (which I also have converted into FASTA files) for each bin with reads extracted by SortMeRNA.
However I am stuck as to what to do next. I assumed I wanted to try to de novo assemble the 16S rRNA sequence from each bin, but I'm at a loss as how to do that as I've never worked with metagenomic data before or performed any de novo assembly.
Does anyone have recommendations as to next steps to try to identify any new genera? I have run the whole metagenome sequence for each bin through GTDBTk to get phylogeny. Is this as good as we can expected to do? Any advice would be greatly appreciated as I try to figure this out. Thanks in advance!