Under COVID, “genome” is no longer an alien word to us. Yet, there is many miles more to go to truly understand the genome as a whole set of heriditary materials, even for academic biologists. A genome sequence assembly is a collection of DNA sequences, which serves as a fundamental resource of any genetic studies, and is ideally contiguous from end to end for each chromosome. However, traditional short-read sequencing cannot span across complex and repetitive regions, demanding for additional complementary data types to build quality genome assemblies. Optical mapping technology is a type of data generated from nanochannel array-based high-throughput fluorescent microscopy, which captures the distances between signals on specific sequence motifs. The signal patterns can then be used to scaffold sequence fragments into ultra-long sequences, even into chromosome-level. Despite the advantage of using optical mapping data to span across repetitive regions inaccessible by sequencing data, and a continuous reliance of visual inspection to examine these regions, there is a lack of available software to extract and viewer built for the purpose. With the optical mapping becoming an integral part of genomic studies, there is a need to allow experimental biologists to quickly access experimental data quality for experimental decisions, as well for bioinformaticians to determine the quality of public datasets for data mining. This presentation will give a brief review on the construction of genome sequence assembly, its challenges and impact, then introduce the use of optical map technology, leading into the development of a Python-built software to create visualization for custom data to be displayed on web app using Plotly & Dash.
If biology is not interesting to you, the optical mapping technology is provided by Bionano Genomics, the stock price of which had risen over 10 times since the end of last year, while I have no affiliation with the company.
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Speaker: Ms. Claire Chung / Hong Kong / The Chinese University of Hong Kong; OSHK; HKOSCON EXCO - GitHub, LinkedIn
Date and Time : October 9, 2021 / 16:30-17:00 (UTC+8)
Academic Bioinformatician; PyConHK speaker in 2017, 2018; Authored on Python Data Visualization