ECA's Bioinformatics Handbook
Preface
1 Introduction
2 Eric’s Notes of what he might do
- 2.1 Table of topics
I Part I: Essential Computing Skills
3 Overview of Essential Computing Skills
4 Essential Unix/Linux Terminal Knowledge
5 Shell programming
6 Sed, awk, and regular expressions
- 6.1 awk
- 6.2 sed
7 Working on remote servers
8 High Performance Computing Clusters (HPCC’s)
II Part II: Reproducible Research Strategies
9 Introduction to Reproducible Research
10 Rstudio and Project-centered Organization
- 10.1 Organizing big projects
- 10.2 Using RStudio in workflows with remote computers and HPCCs
  - 10.2.1 Keeping an RStudio project “in sync” with GitHub
  - 10.2.2 Evaluating scripts line by line on a remote machine from within RStudio
11 Version control
12 A fast, furious overview of the tidyverse
13 Authoring reproducibly with Rmarkdown
14 Managing Workflows with Snakemake
III Part III: Bioinformatic Analyses
15 Overview of Bioinformatic Analyses
16 DNA Sequences and Sequencing
17 Bioinformatic file formats
18 Genome Assembly
19 Alignment of sequence data to a reference genome (and associated steps)
20 Variant calling
- 20.1 Genotype Likelihoods
- 20.2 GATK’s gVCF Workflow
21 Boneyard
22 Basic Handling of VCF files
23 Bioinformatics for RAD seq data with and without a reference genome
24 Processing amplicon sequencing data
25 Variant Annotation
26 Whole genome alignment strategies
- 26.1 Mapping of scaffolds to a closely related genome
- 26.2 Obtaining Ancestral States from an Outgroup Genome
27 An example full workflow from sequences to variants
IV Part IV: Analysis of Big Variant Data
28 Bioinformatic analysis on variant data
V Part V: Population Genomics
29 Topics in pop gen
References
Published with bookdown

Practical Computing and Bioinformatics for Conservation and Evolutionary Genomics

Chapter 11 Version control

11.1 Why use version control?

11.2 How git works

11.3 git workflow patterns

11.4 using git with Rstudio

11.5 git on the command line