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Bioinformatics Workshop for Helminth Genomics (2015) class materials now freely available!

NTDs get some well deserved coverage outside the usual channels: Financial Times Special Report: Neglected Tropical Diseases

Bioinformatics Workshop for Helminth Genomics
(10-11 September 2015)

Genomic approaches are revolutionizing parasitology, including nematology, by taking full advantage of the large amount of sequences generated on Next-Generation Sequencing (NGS) platforms. The number of parasitic helminth genomes is constantly increasing, and the value of this trove of parasitic helminth sequence data is enhanced by the application of bioinformatic tools designed to look for biology in these large volumes of data.

Our lab frequently aids researchers who need to analyze aspects of available data, but more rapid progress in the utilization of this data could be achieved if community members were able to gain experience with next-generation, large-scale analysis methods themselves. Empowering a broader slice of our community with knowledge of these tools and methods will help accelerate progress towards the development of more efficient and sustainable control programs.

It is our hope that training the research community in the computational techniques required will accelerate progress in parasitic helminth research by enabling researchers to formulate and test hypothesis using available and upcoming sequence data on their own.
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Diff. expr. between Adult & iL3 stages of N.americanus

Read alignments in IGV

Visualization of Illumina read quality

Heatmap of diff. expr. genes across stages of B.malayi

Overview of the assembly of PacBio data
The Workshop

Mining gigabase-sized datasets is a major hurdle between data-generation and seeking for Helminth biology in large-scale sequencing projects. This course is designed to address this challenge. Our workshop will teach the computational skills involved in taking raw sequence data, processing it to a cleaned state and then performing some of the more widely-used downstream analyses. The course lasts for 2 days and will be held at The Genome Institute at Washington University in St. Louis over the 10th & 11th of September 2015.

Subjects covered will include:
  • An overview of the data produced by next generation sequencing platforms
  • Data formats, file structures and analytical processing of data
  • Various publicly available analysis tools (eg. components of the Picard toolset, IGV, GATK UG, etc...)
  • Public databases, finding and accessing commonly needed resources
  • De novo assemblies
  • Differential expression analysis
  • identification and annotation of genetic variants in re-sequenced genomes
  • Data visualization of analytical results
  • Sources of help for Bioinformatics analysis
  • Topics of interest to attendees (as time permits)
Intended Participants and Requirements:

Individuals attending this workshop are expected to be researchers whose focus is on helminth infections and whose research will benefit from access and utilization of NGS data of helminth origin. We anticipate having graduate students, postdoctorals, academic faculty members and industrial researchers. Novice bioinformaticians are welcome!

Participants are expected to bring a wifi enabled laptop running Unix (eg. Apple MacBook pro, MacBook Air, etc...) or Linux, or a Windows based machine running Windows 7 or up. Course demonstration material will be provided in a virtual environment that will be run within an Amazon EC2 instance (you'll learn how to connect to this in class). You'll also need to have ssh (for Unix/Linux) or PuTTY (Windows) installed.

Registration and Fee:

Registration is required so that we can prepare the needed resources for students (Amazon EC2 instances, working space, etc...). We'll confirm receipt of your registration form by email to the address provided. Any scheduling changes and/or course information will also be provided to the supplied email. Please be sure that email is correct.

A fee of $150 is required to participate in this workshop. For students planning to attend, sponsorship is available that will cover a one night stay at a nearby hotel (please be sure to let us know you are a student in the Student status question in the regristration form below). Details on how to remit this payment will be posted soon.

Please contact the webmaster at if you have any questions or problems with the form.

NOTICE: Application closed! We have reached our attendance limit of 25 participants. Its possible that the form may be activated again should there be cancellations, so please check back every so often if you want to attend but weren't able to register in time.

Workshop attendance application
Full name:
Student status(students eligible for housing sponsorship):

Suggested Accomodations:

The Parkway Hotel (closest)
4550 Forest Park Ave
St. Louis, MO 63108
Phone: (314) 256-7777
(866) 314-7700

Holiday Inn Express St. Louis Central West End
4630 Lindell Blvd
St. Louis, MO 63108
Phone: (314) 361-4900
Fax: (314) 361-4901

Maps and Directions:

Our address:
The Genome Institute
Washington University School of Medicine
5th floor - Campus Box 8501
4444 Forest Park Ave
St. Louis, MO 63108
Phone: (314) 286-1800
Fax: (314) 286-1810

By Public Transport
You can take the MetroLink to get to The Genome Institute from Lambert Airport.

Get off the train at the Central West End station. Walk east (the same direction as the train you just got off of) to S Taylor Ave. Turn left at S Taylor Ave and walk one short block to Duncan Ave. Turn right on Duncan Ave and walk one block towards Newstead Ave. Before you get to Newstead, you will see a six-story black brick building on the left. The front entrance is on the Newstead side of the building. Take the elevator to the fifth floor and check in with The Genome Institute reception desk (behind the double-glass doors). Call 314-286-1800 if you get lost.

By Car
From the airport, take I-70 east to I-170 south. Take I-170 south to I-64/40 east. Take I-64/40 east until you reach Kingshighway North. Take Kingshighway North (left onto Kingshighway) to Forest Park Ave. Go east on Forest Park Ave (right onto Forest Park). The institute will be 3 blocks from Kingshighway on your right. v4.0           Copyright Statement
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