UA High Performance/High Throughput Computing    

  • Overview of different UA HPC/HTC systems
  • Introduction to Batch job submission and Portable Batch System (PBS)
  • Processing and memory resource requests
  • Data transfer
  • Disk allocations
  • Software modules

NGS analysis software

  • Genome assembly (velvet, SOAPdenovo, Ray, etc.)
  • Transcriptome assembly (Trinity, SOAPdenovoTrans, etc.)
  • Read mapping (BWA, bowtie, etc.)
  • Transcriptome mapping (tophat, gSNAP, etc.)
  • Differential Expression (cufflinks, R/DeSeq, etc.)
  • Variant Discovery (samtools, GATK, etc.)

R Statistical Package

  • Basic R
  • Graphs and plots
  • R Studio