An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates Article Swipe
Ann M. Mc Cartney
,
Medhat Mahmoud
,
Michael D. 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 J. Billingsley
,
Daniel 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 G. Marin
,
Jean Monlong
,
Stephen Price
,
Alejandro R. Gener
,
Jingwen Ren
,
Sagayamary Sagayaradj
,
Nicolae Sapoval
,
Claude Sinner
,
Daniela C. Soto
,
Arda Söylev
,
Arun Subramaniyan
,
Najeeb Syed
,
Neha Tadimeti
,
Pamella Tater
,
Pankaj Vats
,
Justin N. Vaughn
,
Kimberly Walker
,
Gaojianyong Wang
,
Qiandong Zeng
,
Shangzhe Zhang
,
Tingting Zhao
,
Bryce Kille
,
Evan Biederstedt
,
Mark Chaisson
,
Adam C. English
,
Zev Kronenberg
,
Todd J. Treangen
,
Timothy Hefferon
,
Chen-Shan Chin
,
Ben Busby
,
Fritz J. Sedlazeck
·
YOU?
·
· 2021
· Open Access
·
· DOI: https://doi.org/10.12688/f1000research.51477.2
YOU?
·
· 2021
· Open Access
·
· DOI: https://doi.org/10.12688/f1000research.51477.2
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.
Related Topics
Concepts
Benchmarking
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
Identification (biology)
Coronavirus disease 2019 (COVID-19)
Computational biology
Genotyping
Biology
Data science
Library science
Computer science
Medicine
Genetics
Pathology
Ecology
Gene
Infectious disease (medical specialty)
Business
Disease
Marketing
Genotype
Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.12688/f1000research.51477.2
- OA Status
- gold
- Cited By
- 2
- References
- 82
- Related Works
- 10
- OpenAlex ID
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https://openalex.org/W3143667395Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.12688/f1000research.51477.2Digital Object Identifier
- Title
-
An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebratesWork title
- Type
-
preprintOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2021Year of publication
- Publication date
-
2021-09-03Full publication date if available
- Authors
-
Ann M. Mc Cartney, Medhat Mahmoud, Michael D. 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 J. Billingsley, Daniel 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 G. Marin, Jean Monlong, Stephen Price, Alejandro R. Gener, Jingwen Ren, Sagayamary Sagayaradj, Nicolae Sapoval, Claude Sinner, Daniela C. Soto, Arda Söylev, Arun Subramaniyan, Najeeb Syed, Neha Tadimeti, Pamella Tater, Pankaj Vats, Justin N. Vaughn, Kimberly Walker, Gaojianyong Wang, Qiandong Zeng, Shangzhe Zhang, Tingting Zhao, Bryce Kille, Evan Biederstedt, Mark Chaisson, Adam C. English, Zev Kronenberg, Todd J. Treangen, Timothy Hefferon, Chen-Shan Chin, Ben Busby, Fritz J. SedlazeckList of authors in order
- Landing page
-
https://doi.org/10.12688/f1000research.51477.2Publisher landing page
- Open access
-
YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
-
https://doi.org/10.12688/f1000research.51477.2Direct OA link when available
- Concepts
-
Benchmarking, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Identification (biology), Coronavirus disease 2019 (COVID-19), Computational biology, Genotyping, Biology, Data science, Library science, Computer science, Medicine, Genetics, Pathology, Ecology, Gene, Infectious disease (medical specialty), Business, Disease, Marketing, GenotypeTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
2Total citation count in OpenAlex
- Citations by year (recent)
-
2023: 1, 2022: 1Per-year citation counts (last 5 years)
- References (count)
-
82Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.challenges. | 51 |
| abstract_inverted_index.development | 67 |
| abstract_inverted_index.genotyping, | 102 |
| abstract_inverted_index.open-source | 80 |
| abstract_inverted_index.overarching | 36 |
| abstract_inverted_index.Furthermore, | 52, 113 |
| abstract_inverted_index.Pan-genomes, | 29 |
| abstract_inverted_index.advancements | 108 |
| abstract_inverted_index.benchmarking | 110 |
| abstract_inverted_index.improvements | 98 |
| abstract_inverted_index.participants | 139 |
| abstract_inverted_index.<ns3:ext-link | 130 |
| abstract_inverted_index.identification | 85 |
| abstract_inverted_index.</ns3:p><ns3:p> | 34 |
| abstract_inverted_index.community.</ns3:p> | 143 |
| abstract_inverted_index.ext-link-type="uri" | 132 |
| abstract_inverted_index.xmlns:ns4="http://www.w3.org/1999/xlink" | 131 |
| abstract_inverted_index.ns4:href="https://github.com/collaborativebioinformatics/nibSV">https://github.com/collaborativebioinformatics</ns3:ext-link> | 133 |
| cited_by_percentile_year.max | 94 |
| cited_by_percentile_year.min | 89 |
| corresponding_author_ids | https://openalex.org/A5109960687, https://openalex.org/A5037440162, https://openalex.org/A5070603357, https://openalex.org/A5011875082 |
| countries_distinct_count | 8 |
| institutions_distinct_count | 62 |
| corresponding_institution_ids | https://openalex.org/I181547552, https://openalex.org/I4210130836 |
| sustainable_development_goals[0].id | https://metadata.un.org/sdg/15 |
| sustainable_development_goals[0].score | 0.6800000071525574 |
| sustainable_development_goals[0].display_name | Life in Land |
| citation_normalized_percentile.value | 0.49329782 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |