Next-Generation Sequencing Course at MSU

This post originally appeared on the Software Carpentry website.

Analyzing Next-Generation Sequencing Data

June 6th — June 17th, 2011

Kellogg Biological Station, Michigan State University

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

Applications must be received by March 25th for full consideration. See the full announcement at for more information.

Course Description:

This intensive two week summer course will introduce students 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.

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 under a Creative Commons/use+reuse license.

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