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The fifth internati...
The fifth international hackathon for developing computational cloud-based tools and resources for pan-structural variation and genomics
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- Deb, Sontosh K (author)
- University of Alabama
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- Kalra, Divya (author)
- Baylor College of Medicine
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- Kubica, Jędrzej (author)
- University of Warsaw
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- Stricker, Erik (author)
- Baylor College of Medicine
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- Truong, Van Q (author)
- University of Pennsylvania
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- Zeng, Qiandong (author)
- Laboratory Corporation of America Holdings
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- Fiscus, Christopher J (author)
- University of California, Irvine
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- Agustinho, Daniel Paiva (author)
- Baylor College of Medicine
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- Alexander, Adam (author)
- University of North Carolina at Charlotte
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- Arciniega-Sanchez, Marlon (author)
- National Autonomous University of Mexico
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Bosseau, Lorianne (author)
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- Brueffer, Christian (author)
- Lund University,Lunds universitet,Translational Oncogenomics,Forskargrupper vid Lunds universitet,LUCC: Lunds universitets cancercentrum,Övriga starka forskningsmiljöer,Lund University Research Groups,LUCC: Lund University Cancer Centre,Other Strong Research Environments,InSilico Consulting AB
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Canal, Astrid (author)
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Daw, Joyjit (author)
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Enoma, David (author)
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Diaz-Cuevas, Alison (author)
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Diesh, Colin (author)
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Doolittle-Hall, Janet M (author)
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Fernandez-Luna, Luis (author)
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Han, Tina (author)
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Höps, Wolfram (author)
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Huang, Peiming Peter (author)
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Huang, Tony (author)
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Izydorczyk, Michal Bogumil (author)
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Jaryani, Farhang (author)
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Kesharwani, Rupesh K (author)
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Khan, Shaheerah (author)
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Majidian, Sina (author)
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Malakar, Ayan (author)
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Mangolini, Tania Girão (author)
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Modha, Sejal (author)
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Moldes, Mauricio (author)
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Mondal, Rajarshi (author)
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Al Nahid, Abdullah (author)
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Poon, Chi-Lam (author)
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Sagayaradj, Sagayamary (author)
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Sanio, Philippe (author)
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Sepulveda-Morales, Tania (author)
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Shahzaib, Muhammad (author)
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Raza, Muhammad Sohail (author)
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Tat, Trinh (author)
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Thota, Ishaan (author)
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Yaman, Umran (author)
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Yeung, Jason (author)
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Yu, Qiyi (author)
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Zheng, Xinchang (author)
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Mahmoud, Medhat (author)
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Sedlazeck, Fritz J. (author)
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Busby, Ben (author)
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(creator_code:org_t)
- 2024
- 2024
- English.
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In: F1000Research. - 2046-1402. ; 13, s. 1-33
- Related links:
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http://dx.doi.org/10... (free)
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https://lup.lub.lu.s...
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https://doi.org/10.1...
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Abstract
Subject headings
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- BackgroundThe goal of the Fifth Annual Baylor College of Medicine & DNAnexus Structural Variation Hackathon was to push forward the research on structural variants (SVs) by rapidly developing and deploying open-source software. The event took place in-person and virtually in August 2023, when 49 scientists from 14 countries and 8 U.S. states collaboratively worked on projects to address critical gaps in the field of genomics. The hackathon projects concentrated on developing bioinformatic workflows for the following challenges: RNA transcriptome comparison, simulation of mosaic variations, metagenomics, Mendelian variation, SVs in plant genomics, and assembly vs. mapping SV calling comparisons.MethodsAs a starting point we used publicly available data from state-of-the-art long- and short-read sequencing technologies. The workflows developed during the hackathon incorporated open-source software, as well as scripts written using Bash and Python. Moreover, we leveraged the advantages of Docker and Snakemake for workflow automation.ResultsThe results of the hackathon consists of six prototype bioinformatic workflows that use open-source software for SV research. We made the workflows scalable and modular for usability and reproducibility. Furthermore, we tested the workflows on example public data to show that the workflows can work. The code and the data produced during the event have been made publicly available on GitHub (https://github.com/collaborativebioinformatics) to reproduce and built upon in the future.ConclusionsThe following sections describe the motivation, lessons learned, and software produced by teams during the hackathon. Here, we describe in detail the objectives, value propositions, implementation, and use cases for our workflows. In summary, the article reports the advancements in the development of software for SV detection made during the hackathon.
Subject headings
- NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
- NATURVETENSKAP -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Medicinsk genetik (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Medical Genetics (hsv//eng)
- NATURVETENSKAP -- Biologi -- Genetik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Genetics (hsv//eng)
Keyword
- Structural variants
- RNA-seq
- Metagenomics
- Mosaicism
- long-read sequencing
- Hackathon
- NGS
Publication and Content Type
- art (subject category)
- ref (subject category)
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- By the author/editor
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Deb, Sontosh K
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Kalra, Divya
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Kubica, Jędrzej
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Stricker, Erik
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Truong, Van Q
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Zeng, Qiandong
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show more...
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Fiscus, Christop ...
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Agustinho, Danie ...
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Alexander, Adam
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Arciniega-Sanche ...
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Bosseau, Loriann ...
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Brueffer, Christ ...
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Canal, Astrid
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Daw, Joyjit
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Enoma, David
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Diaz-Cuevas, Ali ...
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Diesh, Colin
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Doolittle-Hall, ...
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Fernandez-Luna, ...
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Han, Tina
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Höps, Wolfram
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Huang, Peiming P ...
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Huang, Tony
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Izydorczyk, Mich ...
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Jaryani, Farhang
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Kesharwani, Rupe ...
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Khan, Shaheerah
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Majidian, Sina
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Malakar, Ayan
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Mangolini, Tania ...
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Modha, Sejal
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Moldes, Mauricio
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Mondal, Rajarshi
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Al Nahid, Abdull ...
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Poon, Chi-Lam
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Sagayaradj, Saga ...
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Sanio, Philippe
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Sepulveda-Morale ...
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Shahzaib, Muhamm ...
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Raza, Muhammad S ...
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Tat, Trinh
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Thota, Ishaan
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Yaman, Umran
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Yeung, Jason
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Yu, Qiyi
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Zheng, Xinchang
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Mahmoud, Medhat
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Sedlazeck, Fritz ...
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Busby, Ben
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show less...
- About the subject
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Bioinformatics a ...
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Computer and Inf ...
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and Bioinformatics
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- MEDICAL AND HEALTH SCIENCES
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MEDICAL AND HEAL ...
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and Basic Medicine
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and Medical Genetics
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Genetics
- Articles in the publication
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F1000Research
- By the university
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Lund University