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Old 12-04-2012, 05:26 AM   #1
vl80
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Default Miseq - Bacterial WGS at depth of 10 fold

We are trying to perform bacterial whole genome resequencing using Miseq at a x 10 depth. Has anyone done/ doing this currently at the given depth? Just want to get an idea about the confidence in base calling at such a "low" depth. Saw some recenlt articles appearing in the likes of NEJM with a mean depth of x 11, however a bit worried about the accuracy of the data at this level, specially in handling highly competent bacteria with regions of interest containing mosaic genes.
Any comments/ ideas are most welcome.

Last edited by vl80; 12-04-2012 at 05:29 AM.
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Old 06-25-2013, 08:03 AM   #2
roshanbernard
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Hi,

i am having same concern. though i am using Ion torrent for the same. Any idea what is the ideal coverage i need to maintain to get the accurate results...

if u come across any info, please do share it with me...

thanks in advance

regards
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Old 06-25-2013, 08:15 AM   #3
krobison
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You will get an assembly from this data, but it will be missing a lot of regions due to sampling. Find a good reference on the Lander-Waterman statistics & you can find (or plot) expected completeness vs. coverage statistics.

A rule-of-thumb for resequencing projects in diploids is to shoot for 20X coverage; not sure how much this can be downsampled for haploid organisms.

Also, of course, this is a mean depth -- some regions will be much deeper and some much shallower.
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Old 06-25-2013, 08:33 AM   #4
GW_OK
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A shout out to my old lab:
Lander-Waterman tables
More tables
Even more tables

Last edited by GW_OK; 06-25-2013 at 08:35 AM.
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Old 06-25-2013, 04:44 PM   #5
roshanbernard
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Quote:
Originally Posted by krobison View Post
You will get an assembly from this data, but it will be missing a lot of regions due to sampling. Find a good reference on the Lander-Waterman statistics & you can find (or plot) expected completeness vs. coverage statistics.

A rule-of-thumb for resequencing projects in diploids is to shoot for 20X coverage; not sure how much this can be downsampled for haploid organisms.

Also, of course, this is a mean depth -- some regions will be much deeper and some much shallower.
Thanks a lot for the info...
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