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

Day 1: Linux/TACC Introduction

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
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