Miseq - Bacterial WGS at depth of 10 fold

[vl80]

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.

[roshanbernard]

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

[krobison]

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.

[GW_OK]

A shout out to my old lab:
Lander-Waterman tables
More tables
Even more tables

[roshanbernard]

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...