Teaching basic lab skills
for research computing

Analyzing Next-Generation Sequencing Data

Analyzing Next-Generation Sequencing Data


June 4th — June 15th, 2012
Kellogg Biological Station, MSU
Course sponsor: NIH.

Instructors: Dr. C. Titus Brown, Dr. Ian Dworkin, and Dr. Istvan Albert.

Board of advisors: Dr. Kevin White; Dr. Paul Sternberg; Dr. Rich Lenski; Dr. Robin Buell; Dr. Jim Tiedje; Dr. Lincoln Stein

Applications are being accepted through March 1st (midnight Pacific)!

Course Description

This intensive two week summer course will introduce attendees with a strong biology background to the practice of analyzing short-read sequencing data from Roche 454, Illumina GA2, ABI SOLiD, Pacific Biosciences, and other next-gen platforms. The first week will introduce students to computational thinking and large-scale data analysis on UNIX platforms. The second week will focus on mapping, assembly, and analysis of short-read data for resequencing, ChIP-seq, and RNAseq.

No prior programming experience is required, although familiarity with some programming concepts is helpful, and bravery in the face of the unknown is necessary. 2 years or more of graduate school in a biological science is strongly suggested. Faculty, postdocs, and research staff are more than welcome!

Students will gain practical experience in:

  • Python and bash shell scripting
  • cloud computing/Amazon EC2
  • basic software installation on UNIX
  • installing and running maq, bowtie, and velvet
  • querying mappings and evaluating assemblies

Materials from last year's course are available at http://ged.msu.edu/angus/tutorials-2011 under a Creative Commons/use+reuse license.

You can read a blog post about last year's course at http://ivory.idyll.org/blog/jun-11/ngs-2011.

Dialogue & Discussion

Comments must follow to our Code of Conduct.