very low coverage WGS on Novaseq 6000?

msincan · 11-28-2018, 06:11 PM

Is it possible to multiplex more than 384 samples on a Novaseq 6000 in order to obtain very low coverage WGS (0.5-2x)?

misterc · 11-29-2018, 12:39 PM

You can also use the NovaSeq XP workflow and load 4 different sample pools (1 pool per lane on an S4 flow cell) using the same 384 UDI adapters.

SNPsaurus · 11-29-2018, 08:49 PM

SeqWell has some kits for high multiplexing.

pmiguel · 11-30-2018, 04:30 AM

No reason why it would not be possible. Since you don't specify an organism, I presume you mean a mammal. So you want an average of 3 billion bases/sample. So that would be 1000 UDIs. Presuming you don't want to use the Xp workflow as misterc mentions.

But I'm wondering what misterc means by "the same 384 UDI adapters"? Is he referring to the 384 UDI set generated by Illumina and passed on to their oligo partner, IDT?

Anyway, the issue here, I would think, would be initial oligo cost. You have to drop around $40K to have IDT manufacture a set of 384 UDI adapters. You would have enough to last forever. Whereas, if you were going to use Nextera or Nextera Flex, you could buy step-out primers containing the 384 UDIs for around $6K.

--
Phillip

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11-28-2018, 06:11 PM	#1
msincan Member Location: Maryland Join Date: Dec 2009 Posts: 19	very low coverage WGS on Novaseq 6000? Is it possible to multiplex more than 384 samples on a Novaseq 6000 in order to obtain very low coverage WGS (0.5-2x)?

11-29-2018, 08:49 PM	#3
SNPsaurus Registered Vendor Location: Eugene, OR Join Date: May 2013 Posts: 521	SeqWell has some kits for high multiplexing. __________________ Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

11-29-2018, 12:39 PM	#2
misterc Member Location: Livermore, CA Join Date: Jan 2016 Posts: 44	You can also use the NovaSeq XP workflow and load 4 different sample pools (1 pool per lane on an S4 flow cell) using the same 384 UDI adapters.

11-30-2018, 04:30 AM	#4
pmiguel Senior Member Location: Purdue University, West Lafayette, Indiana Join Date: Aug 2008 Posts: 2,317	No reason why it would not be possible. Since you don't specify an organism, I presume you mean a mammal. So you want an average of 3 billion bases/sample. So that would be 1000 UDIs. Presuming you don't want to use the Xp workflow as misterc mentions. But I'm wondering what misterc means by "the same 384 UDI adapters"? Is he referring to the 384 UDI set generated by Illumina and passed on to their oligo partner, IDT? Anyway, the issue here, I would think, would be initial oligo cost. You have to drop around $40K to have IDT manufacture a set of 384 UDI adapters. You would have enough to last forever. Whereas, if you were going to use Nextera or Nextera Flex, you could buy step-out primers containing the 384 UDIs for around $6K. -- Phillip