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.

More David Duncan's questions See All
Similar questions and discussions