17-20 Dec: Genome Assembly Workshop

Genome Assembly is currently in a renaissance, with new technologies coming together to complement each other, producing high-quality reference grade assemblies. Technologies such as linked reads (10x genomics and Illumina), long read technologies (Pacific Biosciences and Oxford Nanopore Technologies), Hi-C (Dovetail Genomics and Phase Genomics), high-throughput optical mapping (Bionano Genomics), and the corresponding algorithms and methodologies are coming together to produce high-quality genome assemblies.

This workshop will focus on project design, library and sequencing technologies, genome assembly and data type integration process, and evaluation in a practical and informative setting. The format will be approximately half lecture and half practical, using command-line interaction with some R.

Topics will include:

  • An overview of the technologies and how they integrate to produce better genomes

  • Project design and sample considerations

  • Estimating sequencing needs and associated costs

  • QA and QC of raw data

  • kmer analysis using KAT (special guest lecturer Gonzalo Garcia Accinelli, Earlham Institute, UK)

  • Genome Assembly using Falcon and Canu for Pacific Biosciences and Oxford Nanopore

  • Supernova for 10X genomics linked read technology

  • Incorporation of Hi-C data (special guest lecturer Zev Kronenberg, Phase Genomics, US)

  • Genome statistics and evaluating assemblies

  • Discussion on haplotyping genomes: falcon-unzip and falcon-phase

The registration fee is $2,500 for commercial and for-profit participants, $1,200 for other academic or non-profit participants, and $1,000 for UC students, faculty and staff.

Requirements and Prerequisites:  You will need to bring your own laptop to access the assembly computation, which will be performed on the UCD Bioinformatics Core Cluster. Prior 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 not be able to train you in how to use the command-line during this workshop.

For more information, and to register, go to https://registration.genomecenter.ucdavis.edu/

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