F1000Research (Sep 2021)
An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates [version 2; peer review: 1 approved, 3 approved with reservations]
- Ann M. Mc Cartney,
- Medhat Mahmoud,
- Michael Jochum,
- Daniel Paiva Agustinho,
- Barry Zorman,
- Ahmad Al Khleifat,
- Fawaz Dabbaghie,
- Rupesh K Kesharwani,
- Moritz Smolka,
- Moez Dawood,
- Dreycey Albin,
- Elbay Aliyev,
- Hakeem Almabrazi,
- Ahmed Arslan,
- Advait Balaji,
- Sairam Behera,
- Kimberley Billingsley,
- Daniel L Cameron,
- Joyjit Daw,
- Eric T. Dawson,
- Wouter De Coster,
- Haowei Du,
- Christopher Dunn,
- Rocio Esteban,
- Angad Jolly,
- Divya Kalra,
- Chunxiao Liao,
- Yunxi Liu,
- Tsung-Yu Lu,
- James M Havrilla,
- Michael M Khayat,
- Maximillian Marin,
- Jean Monlong,
- Stephen Price,
- Alejandro Rafael Gener,
- Jingwen Ren,
- Sagayamary Sagayaradj,
- Nicolae Sapoval,
- Claude Sinner,
- Daniela C. Soto,
- Arda Soylev,
- Arun Subramaniyan,
- Najeeb Syed,
- Neha Tadimeti,
- Pamella Tater,
- Pankaj Vats,
- Justin Vaughn,
- Kimberly Walker,
- Gaojianyong Wang,
- Qiandong Zeng,
- Shangzhe Zhang,
- Tingting Zhao,
- Bryce Kille,
- Evan Biederstedt,
- Mark Chaisson,
- Adam English,
- Zev Kronenberg,
- Todd J. Treangen,
- Timothy Hefferon,
- Chen-Shan Chin,
- Ben Busby,
- Fritz J Sedlazeck
Affiliations
- Ann M. Mc Cartney
- NIH, Washington, USA
- Medhat Mahmoud
- Baylor College of Medicine, Houston, USA
- Michael Jochum
- Baylor College of Medicine, Houston, USA
- Daniel Paiva Agustinho
- Washington University in St. Louis School of Medicine, St. Louis, USA
- Barry Zorman
- Baylor College of Medicine, Houston, USA
- Ahmad Al Khleifat
- King's College London, London, UK
- Fawaz Dabbaghie
- Institute for Medical Biometry and Bioinformatics, Düsseldorf, Germany
- Rupesh K Kesharwani
- Baylor College of Medicine, Houston, USA
- Moritz Smolka
- University of Vienna, Vienna, Austria
- Moez Dawood
- Baylor College of Medicine, Houston, USA
- Dreycey Albin
- University of Colorado at Boulder, Boulder, USA
- Elbay Aliyev
- Sidra Medicine, Doha, Qatar
- Hakeem Almabrazi
- Sidra Medicine, Doha, Qatar
- Ahmed Arslan
- Stanford University School of Medicine, California, USA
- Advait Balaji
- Rice University, Houston, USA
- Sairam Behera
- Baylor College of Medicine, Houston, USA
- Kimberley Billingsley
- NIH, Washington, USA
- Daniel L Cameron
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Joyjit Daw
- NVIDIA Corporation, Santa Clara, California, USA
- Eric T. Dawson
- NVIDIA Corporation, Santa Clara, California, USA
- Wouter De Coster
- VIB Center for Molecular Neurology, Antwerp, Belgium
- Haowei Du
- Baylor College of Medicine, Houston, USA
- Christopher Dunn
- Pacific Biosciences, Menlo Park, USA
- Rocio Esteban
- Oxford Nanopore Technologies Ltd, Oxford, UK
- Angad Jolly
- Baylor College of Medicine, Houston, USA
- Divya Kalra
- Baylor College of Medicine, Houston, USA
- Chunxiao Liao
- Rice University, Houston, USA
- Yunxi Liu
- Rice University, Houston, USA
- Tsung-Yu Lu
- USC, Los Angeles, USA
- James M Havrilla
- Children’s Hospital of Philadelphia, Philadelphia, USA
- Michael M Khayat
- Baylor College of Medicine, Houston, USA
- Maximillian Marin
- Harvard Medical School, Boston, USA
- Jean Monlong
- UC Santa Cruz Genomics Institute, Santa Cruz, USA
- Stephen Price
- Carnegie Mellon University, Pittsburgh, USA
- Alejandro Rafael Gener
- Baylor College of Medicine, Houston, USA
- Jingwen Ren
- USC, Los Angeles, USA
- Sagayamary Sagayaradj
- University of California, Davis, USA
- Nicolae Sapoval
- Rice University, Houston, USA
- Claude Sinner
- University of Texas at Dallas, Richardson, USA
- Daniela C. Soto
- University of California, Davis, USA
- Arda Soylev
- Konya Food and Agriculture University, Konya, Turkey
- Arun Subramaniyan
- University of Michigan, Ann Arbor, USA
- Najeeb Syed
- Sidra Medicine, Doha, Qatar
- Neha Tadimeti
- NVIDIA Corporation, Santa Clara, California, USA
- Pamella Tater
- DNAnexus, Mountain View, USA
- Pankaj Vats
- NVIDIA Corporation, Santa Clara, California, USA
- Justin Vaughn
- USDA-ARS, Athens, USA
- Kimberly Walker
- Baylor College of Medicine, Houston, USA
- Gaojianyong Wang
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Qiandong Zeng
- Laboratory Corporation of America Holdings, Westborough, USA
- Shangzhe Zhang
- Lanzhou University, Lanzhou, China
- Tingting Zhao
- University of Pittsburgh, Pittsburgh, USA
- Bryce Kille
- Rice University, Houston, USA
- Evan Biederstedt
- Harvard Medical School, Boston, USA
- Mark Chaisson
- USC, Los Angeles, USA
- Adam English
- Baylor College of Medicine, Houston, USA
- Zev Kronenberg
- Pacific Biosciences, Menlo Park, USA
- Todd J. Treangen
- Rice University, Houston, USA
- Timothy Hefferon
- NIH, Washington, USA
- Chen-Shan Chin
- DNAnexus, Mountain View, USA
- Ben Busby
- DNAnexus, Mountain View, USA
- Fritz J Sedlazeck
- Baylor College of Medicine, Houston, USA
- DOI
- https://doi.org/10.12688/f1000research.51477.2
- Journal volume & issue
-
Vol. 10
Abstract
In October 2020, 62 scientists from nine nations worked together remotely in the Second Baylor College of Medicine & DNAnexus hackathon, focusing on different related topics on Structural Variation, Pan-genomes, and SARS-CoV-2 related research. The overarching focus was to assess the current status of the field and identify the remaining challenges. Furthermore, how to combine the strengths of the different interests to drive research and method development forward. Over the four days, eight groups each designed and developed new open-source methods to improve the identification and analysis of variations among species, including humans and SARS-CoV-2. These included improvements in SV calling, genotyping, annotations and filtering. Together with advancements in benchmarking existing methods. Furthermore, groups focused on the diversity of SARS-CoV-2. Daily discussion summary and methods are available publicly at https://github.com/collaborativebioinformatics provides valuable insights for both participants and the research community.
