Depletion of repetitive sequences – WGS libraries

Posted on June 5, 2014 by Marco

As you know, the sunflower genome contains a large amount of repetitive sequences, that is why it is so big and so annoying to sequence. I have been working for a while on optimizing a depletion protocol, to try to get rid of some repetitive sequences in NGS libraries (transposons, chloroplast DNA…). Continue reading →

Genotype By Sequencing (GBS) Barcodes

Posted on November 23, 2012 by Rose

Here are GBS_Barcodes and adapters that we currently have in the lab for GBS, for sequencing on an Illumina machine. They were designed using the site Deena Bioinformatics.

This information came from Greg Baute’s blog and I’ve just converted the file to .xls.

GBS missing data

Posted on November 6, 2012 by Greg B.

I’ve done a small analysis on my GBS data and posted it on my blog: http://www.proseedwithscience.com/?p=816

Edit: This is mostly just a quick look at the amount of missing data in the data and some potential explanations of where it might be from.

Making Illumina Whole Genome Shotgun Sequencing Libraries – (Dan E.)

Posted on March 23, 2012 by Dan E.

I’ve been making whole genome shotgun sequencing libraries (for the purposes of this post: WGSS libraries) to sequence sunflower genomes on the Biodiversity Centre’s Illumina HiSeq. I haven’t been doing it for very long and its likely that my approach will change in the future as costs and products change but, as of early 2012, I’ve landed on a hybrid protocol based on kits from an outfit called Bioo Scientific. I use the Bioo Sci. adapter kit and their library prep kit up to the final PCR step at which point I switch to a PCR kit from another outfit called KAPA. I also use a KAPA kit to quant libraries with qPCR. In this post I give a little context then describe what I do to make WGSS libraries . . . Continue reading →

Illumina Sequencing Adapters (Dan E.)

Posted on March 13, 2012 by Dan E.

I’ve been writing posts about the various steps involved in making WGS sequencing libraries for the Biodiversity Centre’s Illumina HiSeq machine and I was tempted to try to explain what the adapters are for. Then I had the bright idea of seeing if somebody else had already done it. Somebody has. Continue reading →

Illumina Sequencing Adapters and Barcodes (Dan E.)

Posted on March 13, 2012 by Dan E.

As of March 2012 we are using the Bioo Scientific NEXTflex barcoded adapters for WGS sequencing libraries made by ourselves, (well me so far). The set we are currently using comprises 48 barcodes, so we can multiplex up to a 48-plex in one lane on the Illumina HiSeq sequencer.