Old Etherpad link:  https://etherpad.mozilla.org/g2NxIEAFWL

Day 1: Linux/TACC Introduction

• Linux fundamentals
• Getting started at TACC
  • Editing files
  • Stampede profile
  • Piping and redirection

Day 2: Raw Sequencing data manipulation

• Evaluating raw sequencing data
  • Overview of NGS data formats and analyses
  • The FASTA sequencing data format
  • The FASTQ sequencing data format, with Illumina/GSAF-specific details
  • Compression, Linux manipulation of fastq files
  • Overview of sequence quality checking
  • FASTQC - a good place to start
  • FASTX toolkit manipulation of FASTQ data
  • Adapter trimming with cutadapt
  • Batch manipulation of FASTQ files
• Overview of read alignment, references and alignment tools