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RishiDeKayne/README.md

Hi I'm Rishi - a postdoc working at the University of California Berkeley

-I predominantly use genomics to understand the evolution and maintainence of genome-wide variation
-I have worked on a variety of organisms including: 🦈 🦠 🍄 🌴 🐟 🐒
-Among other things I currently work on the evolution of structural variation and aging in 🐟 and 🐒

To find out more about me and my projects you can visit my website or find me on twitter

I primarily code in:

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  1. WhitefishReferenceGenome WhitefishReferenceGenome Public

    Scripts used for whitefish genome assembly/analysis (De-Kayne, Zoller & Feulner 2020)

    Shell 3

  2. LG_to_Chromosome_SyntenyPlots LG_to_Chromosome_SyntenyPlots Public

    This repository contains a custom R script to plot Circos plots using Circlize to identify synteny between linkage groups and chromosomes in a reference genome

    R 3 1

  3. WhitefishLinkageMap WhitefishLinkageMap Public

    Scripts for linkage mapping of C. sp. "Albock" (De-Kayne & Feulner 2018)

    R 2

  4. Danaus_Dchry2.2_annotation Danaus_Dchry2.2_annotation Public

    This repository contains all commands run for the annotation and analysis of the Danaus chrysippus2.2 assembly (Singh & De-Kayne et al. 2022)

    R 1

  5. Alpine_whitefish_WGS Alpine_whitefish_WGS Public

    All scripts associated with the whole-genome sequencing and analysis of 99 whitefish individuals (De-Kayne et al. 2022)

    R 2

  6. GetTEBed GetTEBed Public

    GetTEBed will calculate the TE content in windows along the genome using a genome and the .out file from a RepeatMasker run

    R