Tutorials

Tutorials and useful background reading

Unix command line

• Bash Scripting Tutorial for Beginners

• Speciation & Population Genomics: Getting used to Unix

• Software Carpentry: The Unix shell

• Cornell CBSU Workshop: Linux for biologist

NGS data

• Speciation & Population Genomics: Raw reads exploration

• Cornell CBSU Workshop: Genomic sequence data analysis

RMarkdown

• NTRES 6940: RMarkdown (and the resources linked within)

GitHub

• NTRES 6940: A brief intro to GitHub (and the resources linked within)

• NTRES 6940: Version control and the Git/GitHub workflow (and the resources linked within)

• Version Control w/ Git Tutorial

Genome assembly

• MaSuRCA Quick Start Guide

• Flye Install, Usage, and FAQs

• Carl’s assembly notes in progress

Workflow for low-coverage whole genome sequencing

• Data Processing

• Data Analysis
  

Genome Analysis Toolkit (GATK) Variant Calling

• Genome Analysis Toolkit
  

Directory and code organization

• Directory organization
• Code headers