NGS Summer 2016 – Analyzing Next-Generation Sequencing Data

Posted on Posted in Bioinformatics, Illumina, software, tenure track

August 8 – August 19th, 2016
Kellogg Biological Station, Michigan State University

To Apply: Fill out the form here: Due date 3/1/17

Course Directors:

  • Matt MacManes, Assistant Professor, University of New Hampshire (@macmanes or matthew dot macmanes at unh dot edu)
  • Meg Staton, Assistant Professor, University of Tennessee, Knoxville (@hardwoodgenomic or mstaton1 at utk dot edu)


  • Ian Dworkin, Associate Professor, MacMaster University (@iandworkin )
  • Torsten Seemann, Associate Professor, University of Melbourne (@torstenseemann )
  • Shaun Jackman, PhD candidate, University of British Columbia (@sjackman )
  • Sonal Singhal, Postdoctoral Fellow, University of Michigan.
  • Rob Patro, Assistant Professor, Stony Brook University (@nomad421 )
  • and several others TBA


Feb 8, 2016 – application form is now open! We will close the application period on March 1st (midnight EST) and notify applicants of decisions on March 17th.

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 (e.g., Nanopore, PacBio). The first week will introduce students to computational thinking and large-scale data analysis on UNIX platforms. The second week will focus on genome and transcriptome assembly, transcript quantitation, mapping, and other topics.

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 Trinity, BWA, Salmon, SPAdes, ABySS, Prokka and other bioinformatics tools.
  • querying mappings and evaluating assemblies
  • Materials from previous courses are available at under a Creative Commons/full use+reuse license.

You can read a blog post about the 2015 course here.

What will students learn?

By the end of the course, students will be able to assemble transcriptomes, identify variants, and estimate transcript abundance (from mRNAseq 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, August 8th through 2pm on Friday, August 19th. Morning and afternoon lectures will be interspersed with practical hands-on labs. Room and board will be provided on-site (see enrolling, below). Sunday, August 16th, will be a day of rest & relaxation. Students should expect to arrive at KBS by Monday, August 8th at noon and stay at KBS through Friday, August 19th at 2pm. KBS is several hours away from the nearest large airports (DTW, GRR, LAN) and students coming from out of state should plan on arriving on Sunday.

Applying for the course

An application is required (see here:, and we can accommodate only 24 attendees. We absolutely welcome \”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.

Note that some family housing is available, and there may be child care opportunities as well by special arrangement. Please contact Matt or Meg after you have been admitted to discuss details!

Tuition, course cost, and enrolling

All students must arrange their own transportation to and from KBS and pay for on-site room and board (see prior to arrival.

  • $850 for double occupancy (shared bedroom and bathroom)
  • $1000 for single occupancy (own room, shared bathroom)

This fee covers on-site lodging and weekday meals (see

Applicants must commit to spending both weeks on-site! The middle Sunday will be entirely 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 will not have any additional laptops available this year.

Lodging and family

In 2016, we plan to have housing available for family groups. Child care may be available by arrangement.


Matt MacManes ( holds a Ph.D. in Integrative Biology from UC Berkeley, and has worked in behavioral ecology, population genetics, and more recently transcriptomics and genomics. He is currently an Assistant Professor in Molecular Cellular and Biomedical Sciences at The University of New Hampshire, where his lab works on functional and population genomics in non-model organisms including desert mice, ladybugs, clams, corals, and doves.

Meg Staton ( is an Assistant Professor in the Department of Entomology and Plant Pathology at the University of Tennessee, Knoxville. She specializes in bioinformatics and genomics of plants and her lab helps build the software Tripal, runs genomic data web portals, and analyzes a wide variety of genomics data.

Torsten Seemann ( is an Associate Professor and Lead Bioinformatician at the
Victorian Life Sciences Computation Initiative and the Doherty Centre for Applied Microbial Genomics at the University of Melbourne in Melbourne, Australia. He specializes in developing bioinformatics software tools and pipelines for the analysis of bacterial \”omics\” data, with a focus on applications to clinical and public health microbiology.

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 a faculty member in the Department of Biology at McMaster University, where his lab works on evolutionary genomics of development, morphology and behavior, in addition to the development of new statistical tools.

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 C. Titus Brown.