Next-Generation Sequencing Course 2013

This post originally appeared on the Software Carpentry website.

Analyzing Next-Generation Sequencing Data

http://bioinformatics.msu.edu/ngs-summer-course-2013

June 10th–20th, 2013
Kellogg Biological Station, MSU
Course sponsor: NIH.

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

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 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