index.Rmd

---
title: "Gene-centric mapping of microbial community structure and function"
subtitle: "2020.21 MICB425 Mirobial Ecological Genomics Capstone project"
author: >-
  Stephan Koenig, Kim Dill-McFarland, Connor Morgan-Lang, Ryan McLaughlin, Julia
  Anstett, Resmi Radhamony, Sean Crowe and Steven Hallam
date: "`r format(Sys.time(), '%B %d, %Y')`"
site: bookdown::bookdown_site
documentclass: book
bibliography: book.bib
description: >- 
  A collection of tutorials and the capstone project information for MICB425
  Module 04.
biblio-style: apalike
csl: american-society-for-microbiology.csl
link-citations: true
# See `_output.yml` for output configuration
# See `_bookdown.yml` for other configurations
---

```{r setup, echo = FALSE, warning = FALSE, message = FALSE}
# Saving the default settings for code chunks to use to reset settings
default_chunk_options <- knitr::opts_chunk$get()

library(readr)
library(dplyr)
library(kableExtra)
library(webshot)
```

# Overview {-}

This document introduces bioinformatics workflows useful in gene-centric mapping of functional and phylogenetic anchors encoded in microbial genomes sourced from natural and engineered environments.  

-   Part I outlines the motivation and insights afforded by the use of these workflows to study uncultivated microbial community structure and function.
-   Part II provides hands-on tutorials to learn two effective tools for gene-centric analysis, TreeSAPP and iTOL.
-   Part III described your capstone project to explore primary metagenomic and metatranscriptomic data collected from the Saanich Inlet water column spanning a defined nutrient and energy gradient.