Go Back   SEQanswers > Applications Forums > Sample Prep / Library Generation

Similar Threads
Thread Thread Starter Forum Replies Last Post
DArT seq vs GBS & ddRAD Jayakumar S Bioinformatics 1 04-19-2016 04:10 PM
3000/4000 read 2 GW_OK Illumina/Solexa 33 01-28-2016 08:15 AM
HiSeq 3000/4000 2x150 data scrosby Illumina/Solexa 10 06-04-2015 09:29 AM
Lotsa new toys from Illumina: HiSeq X Five, 3000, 4000, NextSeq 550 GW_OK Illumina/Solexa 53 05-20-2015 11:30 PM
GBS/ddRAD in livestock Jayakumar S Bioinformatics 0 09-29-2014 08:30 PM

Thread Tools
Old 01-17-2017, 01:23 AM   #1
Location: Belgium

Join Date: Apr 2009
Posts: 24
Question ddRAD/GBS lib conc on HiSeq 3000/4000 ?

Hi all,

Has anybody any advice on the "best" concentration (pM) to load a ddRAD or GBS libraries on a HiSeq 3000/4000 ? ddRAD have 300-600 bp, while GBS more around 250-350 bp lib sizes. I know the longer fragments of ddRAD might create a problem may be with the new chemistry/patterned flowcells.

Also 10% Phix would be ok ?


BioGenomics is offline   Reply With Quote
Old 01-17-2017, 02:12 PM   #2
Location: Canada

Join Date: Jun 2013
Posts: 56


The optimal loading concentration and phiX % spike in will likely depend largely on the nucleotide sequence diversity at the start of your reads (on the HiSeq 2000 the first 12 bp is the most critical I think). Depending on how your ddRAD libraries were prepared they may be quite diverse (i.e. balanced proportions of each nucleotide at each position) or suffer from low sequence diversity. From what I read ( the HiSeq 4000 still has low-diversity issues so it would be helpful if you could provide information as to how diverse the start of your reads are. A matrix of the nucleotide diversity for the first 12 bp like the one in the last post of the link below might help others give you recommendations.

After having some run failures last year due to supposed nucleotide diversity issues on a hiseq 2000, we nearly perfect runs by adding some staggered barcodes to break up the restriction site, included a 15% phiX spike in, and clustered at 600-700K/mm^2.
ATϟGC is offline   Reply With Quote

ddrad, gbs, hiseq 4000, library concentration

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 06:11 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO