The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms

Kimberly Walker; Divya Kalra; Rebecca Lowdon; Guangyi Chen; David Molik; Daniela C Soto; Fawaz Dabbaghie; Ahmad Al Khleifat; Medhat Mahmoud; Luis F Paulin; Muhammad Sohail Raza; Susanne P Pfeifer; Daniel Paiva Agustinho; Elbay Aliyev; Pavel Avdeyev; Enrico R Barrozo; Sairam Behera; Kimberley Billingsley; Li Chuin Chong; Deepak Choubey; Wouter De Coster; Yilei Fu; Alejandro R Gener; Timothy Hefferon; David Morgan Henke; Wolfram Höps; Anastasia Illarionova; Michael D Jochum; Maria Jose; Rupesh K Kesharwani; Sree Rohit Raj Kolora; Jędrzej Kubica; Priya Lakra; Damaris Lattimer; Chia-Sin Liew; Bai-Wei Lo; Chunhsuan Lo; Anneri Lötter; Sina Majidian; Suresh Kumar Mendem; Rajarshi Mondal; Hiroko Ohmiya; Nasrin Parvin; Carolina Peralta; Chi-Lam Poon; Ramanandan Prabhakaran; Marie Saitou; Aditi Sammi; Philippe Sanio; Nicolae Sapoval; Najeeb Syed; Todd Treangen; Gaojianyong Wang; Tiancheng Xu; Jianzhi Yang; Shangzhe Zhang; Weiyu Zhou; Fritz J Sedlazeck; Ben Busby

doi:10.12688/f1000research.110194.1

The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms

F1000Res. 2022 May 16:11:530. doi: 10.12688/f1000research.110194.1. eCollection 2022.

Authors

Kimberly Walker¹, Divya Kalra¹, Rebecca Lowdon², Guangyi Chen^{3

4}, David Molik⁵, Daniela C Soto⁶, Fawaz Dabbaghie^{3

7}, Ahmad Al Khleifat⁸, Medhat Mahmoud¹, Luis F Paulin¹, Muhammad Sohail Raza⁹, Susanne P Pfeifer¹⁰, Daniel Paiva Agustinho¹¹, Elbay Aliyev¹², Pavel Avdeyev¹³, Enrico R Barrozo¹⁴, Sairam Behera¹, Kimberley Billingsley¹⁵, Li Chuin Chong¹⁶, Deepak Choubey¹⁷, Wouter De Coster^{18

19}, Yilei Fu²⁰, Alejandro R Gener²¹, Timothy Hefferon²², David Morgan Henke²³, Wolfram Höps²⁴, Anastasia Illarionova²⁵, Michael D Jochum¹⁴, Maria Jose²⁶, Rupesh K Kesharwani¹, Sree Rohit Raj Kolora²⁷, Jędrzej Kubica²⁸, Priya Lakra²⁹, Damaris Lattimer³⁰, Chia-Sin Liew³¹, Bai-Wei Lo³², Chunhsuan Lo³³, Anneri Lötter³⁴, Sina Majidian³⁵, Suresh Kumar Mendem³⁶, Rajarshi Mondal³⁷, Hiroko Ohmiya³⁸, Nasrin Parvin³⁷, Carolina Peralta³⁹, Chi-Lam Poon⁴⁰, Ramanandan Prabhakaran⁴¹, Marie Saitou⁴², Aditi Sammi⁴³, Philippe Sanio⁴⁴, Nicolae Sapoval²⁰, Najeeb Syed¹², Todd Treangen²⁰, Gaojianyong Wang⁴⁵, Tiancheng Xu²⁰, Jianzhi Yang⁴⁶, Shangzhe Zhang⁴⁷, Weiyu Zhou⁴⁸, Fritz J Sedlazeck¹, Ben Busby⁴⁹

Affiliations

¹ Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
² Bayer Crop Science, Chesterfield, MO, 63017, USA.
³ Drug Bioinformatics, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken, Germany.
⁴ Center for Bioinformatics, Saarland University, Saarbrücken, Germany.
⁵ Tropical Crop and Commodity Protection Research Unit, Pacific Basin Agricultural Research Center, Hilo, HI, 96720, USA.
⁶ Biochemistry & Molecular Medicine, Genome Center, MIND Institute, University of California, Davis, Davis, CA, 95616, USA.
⁷ Institute for Medical Biometry and Bioinformatics, University hospital Düsseldorf, Düsseldorf, Germany.
⁸ Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK.
⁹ CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Beijing, China.
¹⁰ Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.
¹¹ Department of Molecular Microbiology, Washington University in St. Louis School of Medicine, St. Louis, MO, 63110, USA.
¹² Research Department, Sidra Medicine, Doha, Qatar.
¹³ Computational Biology Institute, The George Washington University, Washington, DC, 20052, USA.
¹⁴ Department of Obstetrics & Gynecology, Baylor College of Medicine, Houston, TX, 77030, USA.
¹⁵ Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.
¹⁶ Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, Beykoz, Istanbul, Turkey.
¹⁷ Department of Technology, Savitribai Phule Pune University, Pune, Maharashtra, India.
¹⁸ Applied and Translational Neurogenomics Group, VIB Center for Molecular Neurology, Antwerp, Belgium.
¹⁹ Applied and Translational Neurogenomics Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
²⁰ Department of Computer Science, Rice University, Houston, TX, USA.
²¹ Association of Public Health Labs, Centers for Disease Control and Prevention, Downey, CA, USA.
²² National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20892, USA.
²³ Department Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA.
²⁴ EMBL Heidelberg, Genome Biology Unit, Heidelberg, Germany.
²⁵ German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany.
²⁶ Centre for Bioinformatics, Pondicherry University, Pondicherry, India.
²⁷ University of California Berkeley, Berkeley, CA, USA.
²⁸ University of Warsaw, Warsaw, Poland.
²⁹ Department of Zoology, University of Delhi, Delhi, India.
³⁰ University of Applied Sciences Upper Austria - FH Hagenberg, Mühlkreis, Austria.
³¹ Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA.
³² Department of Biology, University of Konstanz, Konstanz, Germany.
³³ Human Genetics Laboratory, National Institute of Genetics, Japan, Mishima City, Japan.
³⁴ Department of Biochemistry, University of Pretoria, Pretoria, South Africa.
³⁵ Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
³⁶ ICAR-NIVEDI, Bangalore, Karnataka, India.
³⁷ Department of Biotechnology, The University of Burdwan, West Bengal, India.
³⁸ Genetic Reagent Development Unit, Medical & Biological Laboratories Co., Ltd., Tokoyo, Japan.
³⁹ Max Planck Institute for Evolutionary Biology, Plon, Germany.
⁴⁰ Weill Cornell Medicine, New York, NY, USA.
⁴¹ Hoffmann-La Roche Limited, Regions, Diagnostics & Research (RDR), Mississauga, Canada.
⁴² Center of Integrative Genetics (CIGENE),Faculty of Biosciences, Norwegian University of Life Sciences, As, Norway.
⁴³ School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh, India.
⁴⁴ University of Applied Sciences Upper Austria - FH Hagenberg, Hagenberg im Mühlkreis, Austria.
⁴⁵ Max Planck Institute for Molecular Genetics, Berlin, Germany.
⁴⁶ Department of Quantitative and Computational Biology,, University of Southern California, Los Angeles, CA, USA.
⁴⁷ School of Biology, University of St Andrews, St Andrews, UK.
⁴⁸ Department of Statistical Science, George Mason University, Fairfax, Virginia, USA.
⁴⁹ DNAnexus, Mountain View, CA, USA.

Abstract

In October 2021, 59 scientists from 14 countries and 13 U.S. states collaborated virtually in the Third Annual Baylor College of Medicine & DNANexus Structural Variation hackathon. The goal of the hackathon was to advance research on structural variants (SVs) by prototyping and iterating on open-source software. This led to nine hackathon projects focused on diverse genomics research interests, including various SV discovery and genotyping methods, SV sequence reconstruction, and clinically relevant structural variation, including SARS-CoV-2 variants. Repositories for the projects that participated in the hackathon are available at https://github.com/collaborativebioinformatics.

Keywords: Cancer; Covid-19; Hackathon; Long-reads; NGS; Structural variants; Tomatoes; Viral integration; k-mer.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Research Support, N.I.H., Intramural
Research Support, U.S. Gov't, P.H.S.

MeSH terms

COVID-19*
Genomics
Humans
SARS-CoV-2* / genetics
Software

Supplementary concepts

SARS-CoV-2 variants

Abstract

Publication types

MeSH terms

Supplementary concepts

Grants and funding