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Vancouver Bioinformatics User Group (VanBUG) » archive for February, 2018

 VanBUG March Event is Cancelled

Due to unforeseen conflicts by both of our March speakers, we are cancelling the March session (March 8th at 6pm).
Please join us in April for Dr. Jared Simpson who has been in the news lately for his work in sequencing the human genome using Oxford Nanopore –
Stay tuned for the April talk announcement! 

 Faraz Hach

Hello everyone, our next event will feature Faraz Hach from the Vancouver Prostate Centre.

Date: February 8th
Time: 6pm
Location: BCCRC ground floor lecture theatre. 675 West 10th Avenue, Vancouver BC

Title: High Throughput Sequencing Data Compression
Abstract: Modern high-throughput sequencing (HTS) platforms generate unprecedented amounts of data that introduce challenges for processing, downstream analysis, and computational infrastructure. As HTS data grow in size, data management and storage are becoming major logistical obstacles for adopting HTS-platforms. One way to solve storage requirements for HTS data is compression. Currently, most HTS data is compressed through general purpose algorithms such as gzip. These algorithms are not specifically designed for compressing data generated by the HTS-platforms. Recently, a number of fast and efficient compression algorithms have been designed specifically for HTS data to address some of the issues in data management, storage and communication. In this talk, I will present solutions to deal with challenges related to storing HTS data.
Bio: Faraz Hach is a Senior Research Scientist at Vancouver Prostate Centre and an assistant professor in department of Urologic Sciences at UBC. In 2013 he received his PhD from Simon Fraser University. His current research involves developing fast and efficient combinatorial algorithms to analyze genomics data generated by Next-Generation Sequencing (NGS) technologies with special focus on structural variations and segmental duplications. He is also interested in designing data structures and algorithms for compressing large quantities of sequencing data to address the challenges related to storage of NGS data. His works have been internationally recognized with several awards and honors. Among these include the Ian Lawson Van Toch Memorial Award for outstanding student paper at the 20th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2012) and the Governor General’s Gold Medal for the best doctoral thesis award from Simon Fraser University in 2014.

Website: Dr. Faraz Hach at Vancouver Prostate Centre

Suggested Reading:
Guillaume Holley, Roland Wittler, Jens Stoye, Faraz Hach: Dynamic Alignment-Free and Reference-Free Read Compression. RECOMB 2017: 50-65
Faraz Hach, Ibrahim Numanagic, S Cenk Sahinalp: DeeZ: reference-based compression by local assembly. Nat Methods. 2014 Nov;11(11):1082-4.
Faraz Hach, Ibrahim Numanagic, Can Alkan, S Cenk Sahinalp: SCALCE: boosting sequence compression algorithms using locally consistent encoding. Bioinformatics 2012: 28(23): 3051-3057

Please note:
Trainees are invited to meet with the VanBUG speaker for open discussion of both science and career paths. This takes place 5:00-5:45pm in either the Boardroom or Lunchroom on the ground floor of the BCCRC


Introductory Speaker:
Phillip A. Richmond (PhD Student, Wasserman lab, CMMT)

Title: Pathogenic noncoding variants in genetic disease
Bio: Phil Richmond is a PhD graduate student in Bioinformatics studying under Dr. Wyeth Wasserman at the BC Children’s Hospital. His research focuses on maximizing the utility of whole genome sequencing in diagnosing rare genetic diseases, with an emphasis on copy number variant calling and noncoding (cis-regulatory altering) pathogenic variants. At BC Children’s Hospital he is involved in multiple clinical efforts that are using this new technology to change how rare genetic diseases are diagnosed. He also has a passion for teaching, and is always looking for teaching assistants for his courses taught through the Compute Canada Education, Outreach and Training committee.


Webcast Link:
(This technology is brought to you by Compute Canada and WestGrid with support from PHSA Telehealth)