As some of you might know, I have been working for the last few months on optimizing a protocol for Illumina WGS libraries that will reduce our dependency on expensive kits without sacrificing quality. The ultimate goal would be to be able to use WGS libraries as a more expensive but hopefully more informative alternative genotyping tool to GBS. Getting to that point ideally requires to develop:
1) A cheaper alternative for library preparation (this post)
2) A reliable multiplexing system (this other post)
3) A way to shrink the sunflower genome before sequencing it (because, as you know, it’s rather huge) (yet another post)
The following protocol is for non-multiplexed libraries. The protocol for multiplexed ones is actually identical, you just need to change adapters and PCR primers – more about that in the multiplexing post.
If you are planning to pool libraries and deplete them of repetitive elements, read carefully all three posts before starting your libraries (mostly because you might need to use different adapters and PCR primers)