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Old 06-08-2015, 07:28 PM   #1
neokao
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Location: USA

Join Date: Mar 2015
Posts: 30
Default shotgun metagenomic sequencing coverage

My lab has been working on bacterial 16S-based microbiome analysis in mouse gut and fecal samples. Recently I've been thinking to move on to Illumina shotgun metagenomic sequencing if we could afford. So I'd like to collect some information to see if it is affordable to my lab.

Assuming there are 20 dominant bacterial species to be assembled,
we will need 20 * 100x (depth for de novo assembling) * 4Mb (estimated size of bacterial genome) = ~8Gb per mouse sample ?

Is the above estimate OK?
Is there any suggestion on the ideal NGS depth and converge needed for each mouse sample ( for fecal or gut bacteria)?

How many mice per condition is recommended?

Could we use the same kit to isolate the fecal bacterial DNA?

Any other concerns on switching from 16S NGS to shotgun metagenomic sequencing?
(I also worried about the bioinformatic part for shotgun metagenomic sequencing)


Thanks.

Last edited by neokao; 06-08-2015 at 07:37 PM.
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