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smsc_2023_conservation_genomics's Introduction

SMSC 2023 Conservation Genomics

We will add important links to this page throughout the course. Readings will be on Dropbox and questions can be asked during class or in Slack.

Hydra Reference Diagram

Hydra reference diagram

Workshop data are in /data/genomics/workshops/smsc_2023/

We will be using a few data sources to learn how to use many different software packages for conservation genomics:

  • Clouded leopard genome assemblies and annotations published in Bursell et al., 2022. One for Neofelis nebulosa and one for Neofelis diardi.
  • PacBio, Hi-C data, and Illumina from a new clouded leopard (Neofelis nebulosa.
  • Illumina short-read data from 4 additional clouded leopards (all Neofelis nebulosa).
  • RNAseq data from multiple tissues of a Red Siskin (Spinus cucullata.
  • Illumina data from 10 Red Siskins from two populations, mapped to a hybrid PacBio/Illumina assembly.

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