Rockfish Species ID via microhaplotyping

Primary Contacts: Anita Wray, [email protected], Krista Nichols [email protected]

Objective:

This project achieved two objectives:

1. Find a sequencing panel to successfully ID rougheye from blackspotted rockfish for the 2025 stock assessment
2. Test additional cryptic species complexes on existing sequencing panels. This repo doesn't include the other panels tested, but we were able to conclude that Diana's GTseq microhaplotyping panel works well.

This work has built off of two other existing repos:

1. Diana Baetscher's species ID GTseq panel & code
2. Eric Anderson's microhaplotyping snakemake

Methods:

1. Run snakemake to call microhaplotypes

Use Eric Anderson's snakemake to call microhaplotypes. See README within the SNAKEMAKE folder for more information

2. Update reference with vouchers

Use Rubias to test if known vouchered specimens can be identified to species using this panel

3. Run unknown samples

Use Rubias to ID unknown samples. For reference, the following are the species that can be identified using this panel.

Also run a PCA:

Disclaimer:

This repository is a scientific product and is not official communication of the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. All NOAA GitHub project code is provided on an 'as is' basis and the user assumes responsibility for its use. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from the use of this GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government.