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.
Hello. We have done that is this paper (not with 16S but with pufM coding scaffolds)
Yutin N, Suzuki MT, Teeling H, Weber M, Venter JC, Rusch DB et al (2007). Assessing diversity and biogeography of aerobic anoxygenic phototrophic bacteria in surface waters of the Atlantic and Pacific Oceans using the Global Ocean Sampling expedition metagenomes. Environ Microbiol 9: 1464-1475.
Marcelino
Hello. We have done that is this paper (not with 16S but with pufM coding scaffolds)
Yutin N, Suzuki MT, Teeling H, Weber M, Venter JC, Rusch DB et al (2007). Assessing diversity and biogeography of aerobic anoxygenic phototrophic bacteria in surface waters of the Atlantic and Pacific Oceans using the Global Ocean Sampling expedition metagenomes. Environ Microbiol 9: 1464-1475.
Marcelino
Marcelino,
Thank you for the reference. That is exactly what I was looking for and your paper lays out the calculations in a very straightforward fashion.
Hi David,
another recent study may also be helpful in this context:
Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities.
http://europepmc.org/abstract/MED/24102695
They essentially extracted 16S reads from Illumina-sequenced metagenomes and analysed how the abundance estimates derived from these 16S "tags" compared to ones that are based on the usual 16S amplicon sequencing.
Hi Georg,
Thank you for this useful reference. I am actually interested in comparing the results from amplicon and shotgun Illumina sequencing, so it will be very helpful to have this study to refer to in my analysis and my manuscript.
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