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 http://bioinformatics.msu.edu/ngs-summer-course-2011 for more information.
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 http://ged.msu.edu/angus/ under a Creative Commons/use+reuse license.