[molecules]

STACKS should be fine.

At the GBS Workshop I attended at Cornell (with speakers including Dr. Buckler), we were told that any tool you can use to analyze RAD data, you can also use to analyze GBS data. So there should be no problem using STACKS for your GBS data.

Also, last I checked bwa and bowtie2 were the aligners mentioned in GBS training by the Buckler group.

disclaimer: I have no experience with STACKS. As part of the Maize Diversity Project, which Ed Buckler heads, I use the Buckler GBS pipeline to work with GBS/RAD maize data.

[Geneus]

STACKS should be fine.

At the GBS Workshop I attended at Cornell (with speakers including Dr. Buckler), we were told that any tool you can use to analyze RAD data, you can also use to analyze GBS data. So there should be no problem using STACKS for your GBS data.

Also, last I checked bwa and bowtie2 were the aligners mentioned in GBS training by the Buckler group.

disclaimer: I have no experience with STACKS. As part of the Maize Diversity Project, which Ed Buckler heads, I use the Buckler GBS pipeline to work with GBS/RAD maize data.

Yes...you are correct...Bowtie2 is what they are using in the GBS pipeline...I got confirmation of that. His lab does however use Novoalign for their WGS.

[jage.g]

Gbs

Hi
my name is Jorge and I student of Biotecnology engineering in Chile. I am think to make a survey of genotyping of Nothofagus dombelyi, and I need to use GBS but I'm not sure which protocol to use, use only one or two restriction enzyme restriction enzymes which are the advantages and disadvantages.