The fifth international hackathon for developing computational cloud-based tools and resources for pan-structural variation and genomics

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Titel: The fifth international hackathon for developing computational cloud-based tools and resources for pan-structural variation and genomics
Autoren: Deb, Sontosh K, Kalra, Divya, Kubica, Jędrzej, Stricker, Erik, Truong, Van Q, Zeng, Qiandong, Fiscus, Christopher J, Agustinho, Daniel Paiva, Alexander, Adam, Arciniega-Sanchez, Marlon, Bosseau, Lorianne, Brueffer, Christian, Canal, Astrid, Daw, Joyjit, Enoma, David, Diaz-Cuevas, Alison, Diesh, Colin, Doolittle-Hall, Janet M, Fernandez-Luna, Luis, Han, Tina, Höps, Wolfram, Huang, Peiming Peter, Huang, Tony, Izydorczyk, Michal Bogumil, Jaryani, Farhang, Kesharwani, Rupesh K, Khan, Shaheerah, Majidian, Sina, Malakar, Ayan, Mangolini, Tania Girão, Modha, Sejal, Moldes, Mauricio, Mondal, Rajarshi, Al Nahid, Abdullah, Poon, Chi-Lam, Sagayaradj, Sagayamary, Sanio, Philippe, Sepulveda-Morales, Tania, Shahzaib, Muhammad, Raza, Muhammad Sohail, Tat, Trinh, Thota, Ishaan, Yaman, Umran, Yeung, Jason, Yu, Qiyi, Zheng, Xinchang, Mahmoud, Medhat, Sedlazeck, Fritz J., Busby, Ben
Weitere Verfasser: Lund University, Profile areas and other strong research environments, Other Strong Research Environments, LUCC: Lund University Cancer Centre, Lunds universitet, Profilområden och andra starka forskningsmiljöer, Övriga starka forskningsmiljöer, LUCC: Lunds universitets cancercentrum, Originator, Lund University, Faculty of Medicine, Department of Clinical Sciences, Lund, Section I, Transl oncogenomics, Translational Oncogenomics, Lunds universitet, Medicinska fakulteten, Institutionen för kliniska vetenskaper, Lund, Sektion I, Transl onkogenomik, Translational Oncogenomics, Originator
Quelle: F1000Research. 13:1-33
Schlagwörter: Natural Sciences, Biological Sciences, Bioinformatics and Computational Biology, Naturvetenskap, Biologi, Bioinformatik och beräkningsbiologi, Computer and Information Sciences, Bioinformatics (Computational Biology), Data- och informationsvetenskap (Datateknik), Bioinformatik (Beräkningsbiologi), Medical and Health Sciences, Basic Medicine, Medical Genetics and Genomics (including Gene Therapy), Medicin och hälsovetenskap, Medicinska och farmaceutiska grundvetenskaper, Medicinsk genetik och genomik (Här ingår: Genterapi), Genetics and Genomics, Genetik och genomik
Beschreibung: Background The 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. Methods As 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. Results The 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. Conclusions The 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.
Zugangs-URL: https://doi.org/10.12688/f1000research.148237.1
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  Data: Background The 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. Methods As 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. Results The 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. Conclusions The 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.
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            – D: 27
              M: 06
              Type: published
              Y: 2024
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