Exome Sequencing on NextSeq500

[sfranzenburg]

Hi,
our lab is currently sequencing human exomes on Ion Proton Sequencers.
Now, we plan to give the NextSeq500 a try (first steps into the Illumina world).

We plan on using the Rapid Capture Exome Kit for whole Exomes and the TrueSight One Kits for clinical exomes.

The aim is to cover >90% of Bases >20x.
How many samples do you pool on a High-Output run (300 cycles) to get reliable exome data? Is 12 a realistic number for whole exomes and 36 for clinical exomes (TrueSight One)?

best,
Sören

[GenoMax]

Have you looked at NextSeq 500 tech specs (http://systems.illumina.com/systems/...cations.html)? These are generally conservative so with good libraries (important) you should be able to get the specified output. You can either calculate backwards or someone else who has done this would give a more direct answer.

[sfranzenburg]

Thank you,
the info that their estimates are conservative is already important for me. Naively I thought these are very optimistic.