Analyzing Next-Generation Sequencing Data
June 10th–20th, 2013
Kellogg Biological Station, MSU
Course sponsor: NIH.
Instructors: Dr. C. Titus Brown, Dr. Ian Dworkin, and Dr. Istvan Albert.
This intensive two week summer course will introduce attendees with a strong biology background to the practice of analyzing short-read sequencing data from Illumina 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
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