Bioinformatics: Genome Assembly and Analysis Workshop [ Pac Bio and 10x Genomics ]

New long (Pacific Biosciences) and linked (10x Genomics) read technologies make 'high' quality genome assemblies affordable and computationally tractable. This workshop will focus on project design, library and sequencing technologies, genome assembly, and evaluation as well as comparative genomics.

The format will be approximately half lecture and half hands-on. The hands-on portion of the workshop will exclusively involve command-line interaction, therefore command-line experience is a must to fully participate. If you are not familiar with the command line but would like to attend, listen, and learn that is OK, but we will be unable to train people how to use the command-line during this short workshop.

Topics will include:

• Technology overview for Pacific Biosciences and 10x Genomics and their differences.
• Project design and sample preparation for both Pacific Biosciences and 10x Genomics
• Estimating needed sequencing and associated costs
• QA/QC of raw data
• Genome Assembly using Falcon for Pacific Biosciences and Supernova for 10x genomics
• Genome statistics and evaluating assemblies
• Discussion on haplotyping genome (falcon-unzip)
• Discussion on comparative genomics

Who should attend? … Anyone who is considering doing a eukaryotic genome assembly project. Bacterial genome assemblies, or metagenomics, will be discussed in a later workshop. Prior workshop participants have included faculty, post docs, grad students, staff, and industry researchers.

What are the prerequisites? … The hands on portion of the workshop will be on the command-line. If you are not familiar with the command line you can still attend, listen and learn. But we will not have time to train participants on how to use the command-line during the workshop.

What do I need to bring? … You will need to bring your own laptop to use, it will need to be able to run Chrome or Firefox, have a recent version of Java installed, and an application that will allow you to ssh into a server (e.g. Putty, or iTerm). Assembly computation will be done on the remote server. We can help with setup early on in the workshop. If your department does not allow you to install software on the laptop you’ll be bringing, please contact us ahead of time.

Can I bring my own data? … No, but we will provide experimental datasets for use during the workshop, as this helps to keep the workshop moving. There will be time, however, to discuss your own datasets and how you might work with them outside of the workshop.

How  much does it cost? … The registration fee is $300 for UC and UC affiliates, $450 for other academic or non-profit participants and $600 for other participants. We accept credit cards, as well as UC Davis recharge accounts, for payment.  Registration fees include light breakfast, lunch, and snacks, but do not include dinner, lodging or parking fees.

Where is the workshop? … It will be held on the UC Davis campus and will run from 9:30am to 4:30pm on the dates indicated, the specific location will be provided a few days before the workshop

How do I apply? … All registration is “first-come, first-served”. There is no application process.  So, sign up as soon as possible to ensure your place in the workshop.

Where can I find more information, including your policies?  ... Go to our website (bioinformatics.ucdavis.edu/training/) and check out our FAQ and Policies.

Questions?

If you have any questions, please don’t hesitate to contact us at training.bioinformatics@ucdavis.edu