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Introduction to NGS analysis

  • Overview
  • Running an interactive job on Raven
  • Setup simulated reads
  • Quality Control
  • Mapping reads
    • Mapping reads using bowtie
    • Mapping reads using bwa
  • Variant discovery
    • Variant discovery on bwa data using GATK
    • Variant discovery on bowtie data using GATK
  • Comparisons between workflows
  • Summary of file formats
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Introduction to NGS analysis

Articles

  • Overview
  • Running an interactive job on Raven
  • Setup simulated reads
  • Quality Control
  • Mapping reads
    • Mapping reads using bowtie
    • Mapping reads using bwa
  • Variant discovery
    • Variant discovery on bwa data using GATK
    • Variant discovery on bowtie data using GATK
  • Comparisons between workflows
  • Summary of file formats
Updated on Fri 23Mar18

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