ksil91

Ostrea_PopStructure

This repository contains code and notebooks detailing analyses of Genotype-by-Sequencing (GBS) data in the Olympia oyster (Ostrea lurida).

Scripts

Scripts for formatting and data analysis.

2016_Notebook

PS-Oly-Larvae-Growth

Repository for paper looking at phenotypic differences among F1 and F2 oysters from 3 populations in Puget Sound, WA.

2bRAD_GATK

Genome-wide reference-based genotyping with 2bRAD

alpheus-gbs

Celegans_RNAprofiling

LMB-panel-2021

Repo for Delta bass manuscript, to be available soon. Still adding some data files and comments to code, but otherwise all there.

Grants

GTseq-Pipeline

A series of perl and python scripts for generating genotypes from NGS fastq files from GTseq library sequencing.

ipyrad

Interactive assembly and analysis of RAD-seq data sets

Ostrea-OA-Repo

Ostrea-Scallop-OA-Repo

PS_CommonGarden

Working repository for project looking at genetic differences among 3 populations in Puget Sound, WA.

Rrunstruct

R package for running the program structure and comparing results from multiple runs

strataG

StrStrataGKS is a modified version of the strataG package by Eris Archer, minimized in order to run Structure without installing too many other packages.

tourmaline

Amplicon sequence processing workflow using QIIME 2 and Snakemake

vcflib

C++ library and cmdline tools for parsing and manipulating VCF files