From claire.wade sydney.edu.au Thu Mar 29 23:13:49 2012
From: Claire Wade <claire.wadesydney.edu.au>
Subject: RE: sheep HD SNP array and MHC typing
Postmaster: Processed by the Listmaster
To: Multiple Recipients of <sheepmodelsanimalgenome.org>
Date: Thu, 29 Mar 2012 23:13:49 -0500
Hi Jennifer, Im not sure that the math adds up below. 5X should be about 15Gb
of mappable data. Often the sequencing produces some level of sludge that
cannot be aligned with the reference. With Illumina HiSeq we can currently do
5X for $1800 and this includes the library preparation. The quote that they
have given you probably excludes the library prep and for us to get this
commercially is worth about $500 per animal (although you can do it yourself
for considerably less). Really in sequencing it is the library prep and
bioinformatics that will remain the cost limiting factors in our experience.
Best wishes,
Claire
Claire Wade | Professor, Chair of Computational Biology and Animal Genomics
Veterinary Science
University of Sydney
RMC Gunn B19-504
Regimental Cres
University of Sydney NSW 2006
AUSTRALIA
claire.wadesydney.edu.au | e
+61 2 9351 8097 |v
+61 2 9351 3957 |f
-----Original Message-----
.From: Thomson, Jennifer [mailto:Jennifer.Thomsonales.ualberta.ca]
.Sent: Friday, 30 March 2012 11:59 AM
.To: Multiple Recipients of <SheepModelsanimalgenome.org>
.Subject: Re: sheep HD SNP array and MHC typing
Excuse my inexperience please, I'm starting as a new prof at Montana State
this year. In shopping for a sequencer for my new lab I am looking at the Ion
Proton machine from LT. It is in early release and can do about 2 whole
genomes at 5x coverage in a single run 10GB of data for $1000- rough estimate
because I don't have the numbers in front of me. They say the next chip will
do 100GB also for $1000. That would be about 6 genomes for $1000 in a single
day run. I think it is a real viable alternative if you have the ability to
process that amount of data.
Jennifer Thomson
Future Asst Professor
Montana State University
Sent from my iPhone
|
