CAUG 2012

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Celera Assembler User Group Meeting

At the J. Craig Venter Institute

Rockville, Maryland, USA

Thursday and Friday, January 12-13, 2012

CAUG 2012 is a 2-day workshop that features presentations, informal discussion, training, and hands-on problem solving. It is an opportunity for users to interact with the developers and other users in order to improve their assembly expertise. CAUG 2010 attracted 30 people including 8 assembly experts.

Conference Notes


9:00 am Light breakfast.
10:00 am Session 1 : Assembly Fundamentals.
  • Presentations by Jason Miller (JCVI) and Dr. Granger Sutton (JCVI).
  • Sequencers and Sequencing strategies.
  • The Logic of the Celera Assembler pipeline.
  • Other assemblers and algorithms.
12:30 Lunch at JCVI.
1:30 pm Session 2 : Applications & User Experiences.
  • Dr. Frank Boellmann (PacBio): The Pacific Biosciences sequencer and software.
  • Sergey Koren (NBACC): Exploiting PacBio data for bacterial genomes.
  • Dr. Haibao Tang (JCVI): Scaffold analysis using genetic maps and comparative genomics for plant genomes.
  • Dr. Doug Rusch (Indiana University): Metagenomes and pushing genome assemblers into environmental sequencing.
  • Dr. Ariel Schwartz (Synthetic Genomics Inc.): Notes from a recent plant genome assembly.
  • Dr. Geoff Waldbieser (USDA-ARS): Fish genomes and confronting many assemblers.
  • Julia Warnke (University of Nebraska): Design and test of an alternate unitig algorithm.
5:00 pm Meeting adjourn
6:00 pm Restaurant dinner.
8:30 am Light breakfast.
9:00 am Session 3 : CA version 7
  • Presentations by Brian Walenz (JCVI) and Jason Miller (JCVI).
  • Code fixes, new features, known issues.
  • New code to classify Illumina mate pairs..
  • Unitig modules, old and new.
  • QC reports, posmap files, and other CA outputs.
  • Valid inputs and options for running CA.
  • Launch an assembly for the workshop.
12:30 Lunch at JCVI.
1:30 pm Session 4 : Workshop.
  • Workshop led by Brian Walenz (JCVI).
  • Review assembly results.
  • Using CA stores, logs, and utilities.
  • Troubleshooting a failed assembly.
  • Parallel computing, grid submissions.
  • Integrating Sanger, 454, Illumina, and PacBio.
  • Future directions: trimming, correcting, and classifying.
3:30 pm Optional tour of JCVI.
4:00 pm Box meal to go.


This meeting is made possible by a grant from the National Institute of General Medical Sciences (NIGMS), one of the United States National Institutes of Health (NIH).

Conference Logistics

Registration Required

NEW ON JANUARY 9: The meeting is fully booked. If you are registered, then you have received a blue & white form from JCVI that says "This is your confirmation of registration." If you have questions, please send email to ATGatJCVIdotORG (but fix up that email address).

No Tuition

There is no tuition for this event. Light breakfast and lunch will be provided, plus one group dinner.

Travel Reimbursement

There are limited funds for travel+hotel reimbursement. Funds are sufficient to cover USA domestic air fare and local lodging for two nights. Reimbursement will be awarded to the first 15 non-local registrants. These attendees will make their own travel arrangements and submit receipts. Contact us for details.

Near Washington DC

The J. Craig Venter Institute (JCVI) is located in Rockville MD USA. (City = Rockville, County = Montgomery, State = Maryland, Country = USA.) Rockville is 20 miles (33 km) north of Washington D.C. Washington is a very good tourist destination featuring the free Smithsonian museums. The Metro Rail red line from Rockville takes less than an hour to reach downtown. The Metro stop (Shady Grove) is a 15 minute bus ride from JCVI in Rockville.

Travel Tips

AIRPLANES: JCVI is equidistant from the three Washington-area airports: BWI Marshall International, IAD Dulles International, and DCA Reagan National. The trip is under one hour, though DC traffic can slow you down. There is a brand new toll road called ICC that probably makes the BWI trip shortest.

AIRPORT TRANSPORTATION: There are no trains from either international airport!!!! There are taxi and shuttle services at all the airports. The drive will take under one hour unless DC traffic slows you down. You would be wise to arrange your shuttle in advance with a company such as Super Shuttle or ABC Limo. There are trains at the national airport, DCA (see below). To enable sharing of rides, we will advise you if others will be arriving at approximately the same time and place.

TRAIN TO AIRPORT: The DC Metro goes to Reagan National Airport only. Take the Red Line to Shady Grove. The Red Line goes in two directions, so make sure your train is headed toward Shady Grove! Go to Shady Grove station, the last stop on the Red Line. DC Metro Train Map. It is a 15-minute drive from Shady Grove station to JCVI. See below about bus, taxi, and walking options.

WALKING FROM TRAIN: The walk between JCVI and the Shady Grove metro requires almost an hour. It is made unpleasant by the need to cross over the highway. Google suggests this route.

BUS FROM TRAIN: The Montgomery County Ride On bus runs between JCVI and the Shady Grove Metro train station. See the Bus 43 schedule. Bus 43 runs from the Shady Grove metro station to Shady Grove Hospital. The hospital is on Medical Center Drive, right across the street from JCVI. The bus runs every 15 minutes at rush hour and every 30 minutes at other times.

TAXI FROM TRAIN: There are taxis waiting at the Shady Grove train station at all times. Expect a 15 minute drive from the station to JCVI. For return to the train station after the meeting, JCVI will call taxi cabs for participants.

DRIVING TO JCVI: Directions to the JCVI main campus. Traffic can be bad on I-270, the nearby highway. County Traffic Cam includes our highway exit, Shady Grove.

CAMPUS: The office is in a 5-building complex. Our building is marked 9704 in tiny numerals that are hard to spot. Our building is the tallest building in the complex and it has 4 colors of glass reminiscent of chromatograms.

TEMPERATURES: Check the weather forecast. Winter time is usually cold (~30 F = 0 C). A few inches of snow is common. The indoor facilities are usually cool (68 F = 20 C) so consider bringing long sleeves or even a sweater. Meeting dress code is: CASUAL! Open toed shoes are not allowed on the lab tour.

HOTEL: The nearest hotel is the Hilton Garden Inn ( Corporate web site. Address = 14975 Shady Grove Road, Rockville, Maryland USA 20850. Telephone: 240-507-1800.) Contact us if you would like to receive a list of other nearby hotels. Attendees may want to fly in Wednesday night and fly out Friday night (two nights in the hotel). Attendees may want to remain in the area to tour Washington before or after the meeting.