I'm looking at using 16S rDNA from a short-read shotgun metagenome to look at bacterial community composition. Along with a large number of single read sequences, I have a smaller number of assembled 16S sequences.
Is there a good way to estimate how many reads are represented by each assembled contig? The best I've been able to come up with is:
gene length x read depth / mean singleton length
but this seems overly simplistic.
Thank you in advance for any ideas.