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100,000 Genomes Project in Wales - Bioinformatics Training

Introduction to Genomic Technologies

  • Ethics issues with genomic sequencing
  • Genomics in research
  • Next Generation Sequencing
  • NGS Technologies
  • Panel, Exome and Whole Genome Sequencing
  • SNP and indel theory

Introduction to Clinical Genomics

  • Clinical annotation of variants
  • Clinical applications of genomics
  • The 100,000 genomes project in Wales

Introduction to Genomic Data

  • Data management for genomics
  • Experimental designs for variant calling
  • NGS data formats and tools
  • Overview of human reference genomes
  • Public sequencing repositories

Bioinformatics Practicals

  • Advanced variant calling
  • Basic variant calling
  • Creating pipelines for variant discovery
  • High throughput annotation of variants
  • Manual annotation of variants
  • Mapping reads to a reference genome
  • Quality control of NGS reads
  • Variant filtering
  • Visualising NGS data and analysis results

Computing Skills Practicals

  • Bash scripting
  • Connecting to Supercomputing Wales
  • Filtering data with Excel
  • Introduction to the UNIX command line
  • Jobs and queuing on HPC systems
  • Redirection and piping
  • Working with containers
  • Working with text files

Additional Topic Primers

  • ChIP-seq analysis
  • RNAseq analysis
  • The R environment for statistical computing
  • Variant calling in transcriptomes
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