MSU NGS Summer Course 2013

Analyzing Next-Generation Sequencing Data

June 10th - June 20th, 2013
Kellogg Biological Station, MSU

Please sign up for the announcements mailing list if you are interested in taking this class in the future; also see the 2014 announcement.

Course sponsor: NIH.

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

The course materials are freely available under a Creative Commons license.


Apr 3, 2013 — We sent out decisions. If you haven't received one, check your spam folder and the contact us. Applications are closed - and we have a long waiting list!

Mar 23, 2013 — We received over 200 applications this year, and are still working our way through them. No decisions have been made yet.

Mar 1, 2013 — Course applications are closed, and we are not taking any further names. See the list of other workshops and courses if you are still interested in training.

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

Materials from previous courses are available at under a Creative Commons/use+reuse license.

You can read a blog post about the 2012 course here.

What will students learn?

By the end of the course, students will be able to map short-read data to sequenced genomes and query the mapping for variation, transcript prevalence (from mRNAseq data), and enriched genomic regions (from ChIP-seq data). They will also know how to transfer large data sets between computers, run extended analyses while asleep, execute and modify existing Python scripts, and otherwise effectively make use of basic computational resources.

Location, dates, and course structure.

The course will be held at the W.K. Kellogg Biological Station on Gull Lake in western Michigan from noon on Monday, June 10th through noon on Friday, June 20th. Morning and afternoon lectures will be interspersed with practical hands-on labs. Room and board will be provided on-site (see enrolling, below). Sunday, June 16th, will be a day of rest & relaxation. Students should expect to arrive at KBS by Monday, June 10th at noon and stay at KBS through Friday, June 20th at 2pm. KBS is several hours away from the nearest airports and students coming from out of state should plan on arriving on Sunday.

Applying for the course

An application is required, and we can accommodate only 24 attendees. We welcome people unaffiliated with MSU, and "students" of any career stage, including postdocs and faculty. Applicants are not selected on a first-come-first-serve basis, and we try to create a balanced class of participants.

Apply here! Applications close Feb 28th, 2013, at midnight EST.

We'll confirm receipt of your application by Friday, March 1st; if you don't hear from us by then, check your spam folder and then contact Titus Brown at ude.usm|btc#ude.usm|btc.

Tuition, course cost, and enrolling

All students must pay for on-site room and board (see Orchard Dorms) upon arrival. It should be about $500. We will make arrangements for housing *after* choosing students.

There is no tuition fee. All course materials and sundry expenses will be covered.

Applicants must commit to spending both weeks on-site! The middle Sunday will be free.

Taking the course for-credit

There is no formal option for taking the course for credit at MSU or elsewhere.


Please plan to bring a laptop (Mac OS X, Windows, or Linux are all OK). We do not have any additional laptops available this year.


C. Titus Brown ( holds a Ph.D. in Developmental Biology from Caltech, and has worked on digital evolution, physical meteorology, developmental biology, and genomics. He is currently an Assistant Professor in Computer Science and Engineering, and Microbiology and Molecular Genetics, at Michigan State University, where his lab works on developmental biology, genomics and metagenomics data analysis, and software tool development.

Ian Dworkin ( holds a Ph.D. in Evolutionary Genetics from the University of Toronto, and has worked on Quantitative and statistical genetics, Evolutionary biology, genomics and developmental biology. He is currently an Associate Professor in Zoology, and in the Program in Ecology, Evolutionary Biology and Behavior, at Michigan State University, where his lab works on evolutionary genomics of development, morphology and behavior, in addition to the development of new statistical tools.

Dr. Istvan Albert ( holds a Ph.D. in Physics from the University of Notre Dame and has worked in statistical physics, data mining, bioinformatics and genomics. He is currently an Associate Professor in Biochemistry and Molecular Biology at the Pennsylvania State University where his group works on developing novel data analysis and visualization methods in the fields of bioinformatics and medical informatics. He is also the maintainer of BioStar, a question and answer site for bioinformatics research:

Board of Advisors

Human genetics and genomics: Kevin White, James and Karen Frank Family Professor at University of Chicago.

Animal genetics and genomics: Paul W. Sternberg, Thomas Hunt Morgan Professor of Biology at the California Institute of Technology; member of the National Academy of Sciences.

Microbial evolution and resequencing: Richard E. Lenski, Hannah Distinguished Professor at Michigan State University; member of the National Academy of Sciences.

Plant genetics and genomics: Robin Buell, Associate Professor at Michigan State University.

Microbial population sequencing and metagenomics: James M. Tiedje,
Professor, Michigan State University; member of the National Academy of Sciences.

Bioinformatics and genomics: Lincoln Stein, Platform Leader, Informatics and Bio-Computing, Ontario Institute for Cancer Research; Professor, Cold Spring Harbor Laboratory.


This course uses materials developed under AFRI Competitive Grant no. 2010-65205-20361 from the USDA NIFA, and is supported by Grant Number R25HG006243 from the National Human Genome Research Institute, both to CTB.

Other courses and workshops

A somewhat current list of workshops and courses

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