Next-gen sequencing

From academy

This course will provide computational training required for those working with Next-generation sequencing data and is aimed in particular at senior graduate students, research fellows and faculty that are producing genomic data. The course aims to lower the learning curve and increase familiarity of wet-lab scientists with informatic techniques. We will cover manipulation of next-gen sequencing data, analysis of metagenomic data, phylogeny reconstruction from NGS and RNA quantification with and without a reference genome. We will use tools such as Amazon EC2, Galaxy, Geneious, SAMtools, QIIME, Trinity RNA-Seq, edgeR, TopHat, LOX and PhyDesign.

At the end of this course, participants will

• have a concrete understanding of the general power and limitations of NGS
• understand which tools should be used and why
• be able to address biological questions of interest using the raw data from the sequencing machine.

An added advantage of attending will be networking and the creation of a community of researchers familiar with an inter-operable set of tools, providing continued support and the potential for collaboration into the future.

Please, visit again this wiki for regular updates.

We also offered this course in 2011. You can check out the page from last year's course to see the content and course materials.

Sponsorship

Computational resources for this course will be available through the Amazon Web Services Education Grants Program. Complementary 8-week licences for Geneious are provided by BioMatters.

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Applications

Applications are now closed. The deadline for applications was Friday, March 9, 2012. We expect that admission will be competitive, so your application is not a guarantee of a space in the workshop. We will select applicants based on answers to the application questions, and also based on demographic and career stage diversity among the participants. If you have any questions about the application process, please contact academy@nescent.org.

Instructors

Instructors from diverse backgrounds will lead students through lectures and practicals designed to give students concrete experience working with a diverse set of analysis tools and techniques.

• Greg Caporaso (QIIME; Northern Arizona)
• Jose Carlos Clemente Litran (QIIME, University of Colorado)
• Francesc López (Fungal phylogenomics and gene expression; Yale)
• Alexie Papanicolaou (Non model species genomics; CSIRO, Australia)
• Konrad Paszkiewicz (Prokaryote Genomics and Sequencing Service; U. Exeter, UK)
• Sergei L Kosakovsky Pond (viral genomics, HyPhy, Galaxy; UC San Diego)
• Jeffrey Townsend (Fungal phylogenomics and gene expression, Yale)
• Lectures will be given by visiting scientists

Dates

The course will be held from June 11-19, 2012 at the National Evolutionary Synthesis Center in Durham, NC.

Costs

Tuition is $600. Participants are responsible for their own travel costs, including transportation and accommodation. A limited number of travel scholarships from NESCent are available for US-based students. Preference will be given to students from under-represented minorities.

Travel

Plan to arrive Sunday, June 10 and leave no earlier than 6 pm on Tuesday, June 19. The Raleigh-Durham airport is located approximately 15 miles from central Durham. Ground transportation to and from the airport is not included in the course registration, but taxi service is readily available, or you can arrange shared rides with other participants using the course email listserv.

Accommodations

NESCent has reserved a block of rooms at Duke Tower for participants and instructors. Please mention NESCent when booking your room. The rooms are suite-style, with a separate living room and kitchen. Some rooms have two double beds, if some of you want to share a room to reduce costs. There is a free shuttle between NESCent and Duke Tower, or the hotel is a 25 minute walk (map) through the lovely Trinity Park neighbourhood and East Campus. You are, of course, free to choose alternate accommodations in Durham.

Parking

For local participants who will be driving to NESCent, you can park in the "Duke Visitor" spaces at the Erwin Mill building - the long, red brick building at 2024 W. Main St, just west of the Wells Fargo at 9th St and Main St. The NESCent entrance is Bay A, closest to Main St. Please pick up a parking pass at the front desk on Monday morning - cars parked in visitor parking for multiple days without a permit will be ticketed and possibly towed.

Meals

NESCent will provide coffee, tea and juice throughout the day. There are many restaurants within a 5 minute walk of NESCent, and Duke Tower is also within walking distance of many restaurants in downtown Durham. The Durham page lists some options for food and drink.