Bioinformatics Crash Course - July 2014

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2014 Summer Workshop Schedule


Bioinformatics Crash Course

July 21-25, 2014

This new workshop will teach participants about the latest Next Generation Methods, Tools, and Techniques and will cover:

  • NGS Sequencing Platforms (Illumina, Pac Bio, etc)
  • Raw data quality control and processing
  • De novo genome assembly
  • RNA-seq differential expression analysis
  • Transcriptome assembly
  • Variant detection (SNP and indels)
  • Cloud Computing
  • Experimental Design
  • Linux and python training 
  • HPC utilization and job submission
This hand-on workshop will provide training on the most common aspects of NGS analysis and methodology. Participants should have an understanding of general biological concepts but no bioinformatics knowledge is required. The course will begin with an introduction to the command line and using High Performance Computer Clusters (HPCC, DeepThought2). By combining lectures with hands-on examples participants will gain an understanding of the most common bioinformatic workflows and tools. 

Who should attend: Undergrads, Grad Students, Post-docs, and Faculty that want to learn the basic tools and techniques involved in NGS analysis and bioinformatics. 

This workshop will be held at UMD-College Park from 9-4pm and registration includes lunch and all course materials. 

Registration fee:

$500 - UMD-CP affiliates

$625 - Non-UMD-CP affiliates 


Day 1

Introduction PPT 

Linux Training

Day 2 

NGS PPT

Steve Mount Sailfish Documents

RNAseq PPT

Day 3

Assembly PPT

MIhai Pop PPT

Mihai Pop tutorial 

Mihai Pop files 

Read QC guide 

Day 4

Assembly workflow guide

Matt Conte PPT

Matt Conte PacBio guide 

Day 5 

Assembly kmer test

MAKER tutorial

Install local BLAST+