Stacks Nature Protocols paper

[Julian Catchen]

Hi All,

Our protocol for running the 1.XX Stacks pipeline has been published
today in Nature Protocols:

https://www.nature.com/articles/nprot.2017.123

If you don't have institutional access you can view the paper here:

http://rdcu.be/z0xm

or write the authors for a PDF.

This work was done by my postdoc Nicolas Rochette and myself; I'm sure
you have seen him answering lots of questions on the mailing list. This
protocol represents an idealized method for running the pipeline for
both de novo and reference-aligned data. Although we couldn't get all of
the information in here, we tried to cram in all the tricks we could
think of (primarily in the 'boxes' of the manuscript).

Also, this paper builds on, and incorporates, the work of Josie Paris
published in her Lost in Parameter Space paper:

http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12775/full

These two papers represent most of what we know having worked on this
type of data for a while, although we are constantly learning new things
that we don't know.

Best,

julian

[Julian Catchen]

ps - the scripts to run the pipeline as described in the manuscript are
open source:

https://bitbucket.org/rochette/rad-seq-genotyping-demo/src/

and sample data can be downloaded here:

http://catchenlab.life.illinois.edu/data/rochette2017_gac_or.tar.gz

[Brenna Levine]

Hi Julian and Nicolas,

I just wanted to tell you how helpful I have found this paper to be. Thanks for publishing your protocol!

Regards,

Brenna Levine

PhD Candidate

University of Arkansas

[mht]

Hi Julian and Nicolas,

Both very interesting and helpful papers. The "Lost in parameter space" paper talks about integrated method (de novo + ref) and it seems to be the better approach if one has a reference genome available.
I see some helpful threads here, but was wondering if there is any reason it's not included or discussed in the other paper or even the Stacks manuals? Is it still in the experimental stages of development?

Cheers,
Mun

[Krishna Mohan]

Julian and Nicholas,

This paper is great!

We have started using stacks v2b as you improved upon the SNP calling. I would appreciate to see similar paper on stacks v2.

Regards,

Krishna

[Julian Catchen]

Hi Mun,

I recommend the integrated approach if you have a draft genome. There is
no specific reason for the level of documentation, just the amount of
time we have had to do it.

Best,

julian