Lab02.qmd

---
title: "Lab02: Design a Genome Project"
bibliography: references.bib
csl: nature.csl
lang: en-US
---

## Lab 2 {#sec-lab02}

In Chapter 1, we introduced three broad perspectives on bioinformatics and genomics (cell, organism, tree of life) [@pevsner2015]. Later in the textbook, Pevsner expands these 3 perspectives into five basic perspectives on genome sequencing.

For this lab, you will use these 5 perspectives, along with your new understanding of sequencing technologies from Chapter 2, to sketch a 1–2 page narrative for a hypothetical genome project [@pevsner2015; @vandijk2018; @vandijk2023]. 

The five perspectives on genomics discussed in Pevsner Chapter 15 can be summarized as:

-   **Catalog genomic information**: basic genome features (size, chromosomes, GC content, repeats, gene counts), based on sequencing, assembly, and annotation.
-   **Catalog comparative genomic information**: whole‑genome comparisons to related species, orthologs, divergence times, lateral gene transfer, using whole‑genome alignments and genome browsers.
-   **Biological principles**: how genome structure and variation underlie development, metabolism, behavior, and evolutionary processes (e.g., genome size evolution, polyploidization, gene birth/death).
-   **Human disease relevance**: how genomes relate to disease in humans or plants, including SNPs, linkage and association studies, and host–pathogen interactions.
-   **Bioinformatics aspects**: databases, software, and visualization tools that make genome analysis possible.

These map naturally onto the three perspectives in Chapter 1: cell‑scale questions, organism‑level questions, and tree‑of‑life/comparative questions [@pevsner2015].

### The Assignment

Write a 1–2 page narrative of the genome analysis project you have designed. To guide you, begin by reflecting on the following questions:

- _If you could sequence the genomes of 100 individuals from any species, which species would you choose?_ 
- _What hypotheses would you test, how would you perform data analyses, and what resources would you require in terms of hardware, software, and collaborators?_ 
- _What ethical issues might arise in sequencing these genomes?_

Specifically, think about: 

- Which sequencing platforms and coverage would you choose (Chapter 2)? 
- Which file formats and QC steps would your workflow rely on (Chapter 3)? [@pevsner2015; @vandijk2018; @vandijk2023]

For your design narrative: 

- Choose a species and justify why 100 genomes from this species would be informative. - State one or two main hypotheses, or guiding questions if discovery-based. 
- Identify which of the five perspectives (and which of the three Chapter 1 perspectives) your project emphasizes. 
- Outline your sequencing strategy (platforms, approximate coverage, sample types) using concepts from Chapter 2. 
- Sketch the main analysis steps (from raw FASTQ through alignment/assembly and downstream analyses) using ideas from Chapters 1 and 3. 
- Briefly note any major ethical issues if humans or other sensitive species are involved.

The focus of your design narrative should be on **motivation and approach**. You may refer to assigned readings (e.g., @hotaling2021; @marks2021; @bogan2025) in your narrative, but you do not need a formal reference list.

## References

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