New Protocol Paper for Stacks 2

[Angel Rivera-Colón]

Hello Stacks users,

I am very excited to announce a new protocol for Stacks 2 that Julian Catchen and I developed over the last few months. The preprint for the protocol, “Population genomics analysis with RAD, reprised: Stacks 2” is now available on BioRxiv: https://doi.org/10.1101/2021.11.02.466953. Please check it out.

The manuscript is conceptually similar to the Stacks 1 protocol published a few years ago (Rochette & Catchen 2017), but it focuses on many of the new approaches available in Stacks 2, such as processing paired-end reads, removing PCR duplicates, and generating longer haplotypes from the paired-end loci. It provides a step-by-step approach of the pipeline, including processing raw reads, de novo parameter optimization, and analysis with both de novo and reference-based approaches. We provide some examples on how to generate some of the commonly used outputs of `populations`, including how to filter, generating whitelists, etc. Also, we show to access a lot of very useful information from the logs using the `stacks-dist-extract` tool. If you haven’t used it already, I highly recommend checking the protocol as it makes exporting things like coverage, PCR duplicate rates, and missing data very easy.

Very importantly, we have a section on troubleshooting. We address some common issues found during analysis, such as issues with trimming reads, and how to address low coverage, for example. Some of these ideas came from discussions we have previously seen in this forum, so I would like to thank you all for your participation here.

We hope the protocol is very useful for your current and future RADseq experiments using Stacks.

Angel G. Rivera-Colón
PhD Candidate
Catchen Lab
Department of Evolution, Ecology, and Behavior
University of Illinois at Urbana-Champaign
@arcolon14