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

Deb, Sontosh K ; Kalra, Divya ; Kubica, Jędrzej ; Stricker, Erik ; Truong, Van Q ; Zeng, Qiandong ; Fiscus, Christopher J ; Agustinho, Daniel Paiva ; Alexander, Adam and Arciniega-Sanchez, Marlon , et al. (2024) In F1000Research 13. p.1-33
Abstract
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... (More)
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. (Less)
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organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Structural variants, RNA-seq, Metagenomics, Mosaicism, long-read sequencing, Hackathon, NGS
in
F1000Research
volume
13
article number
708
pages
1 - 33
publisher
F1000 Research Ltd.
ISSN
2046-1402
DOI
10.12688/f1000research.148237.1
language
English
LU publication?
yes
id
10ab48f5-5b60-4df6-9041-f926d7637d9f
date added to LUP
2024-08-20 17:07:15
date last changed
2024-08-21 07:24:24
@article{10ab48f5-5b60-4df6-9041-f926d7637d9f,
  abstract     = {{Background<br/><br/>The goal of the Fifth Annual Baylor College of Medicine &amp; 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.<br/><br/>Methods<br/><br/>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.<br/><br/>Results<br/><br/>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.<br/><br/>Conclusions<br/><br/>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.}},
  author       = {{Deb, Sontosh K and Kalra, Divya and Kubica, Jędrzej and Stricker, Erik and Truong, Van Q and Zeng, Qiandong and Fiscus, Christopher J and Agustinho, Daniel Paiva and Alexander, Adam and Arciniega-Sanchez, Marlon and Bosseau, Lorianne and Brueffer, Christian and Canal, Astrid and Daw, Joyjit and Enoma, David and Diaz-Cuevas, Alison and Diesh, Colin and Doolittle-Hall, Janet M and Fernandez-Luna, Luis and Han, Tina and Höps, Wolfram and Huang, Peiming Peter and Huang, Tony and Izydorczyk, Michal Bogumil and Jaryani, Farhang and Kesharwani, Rupesh K and Khan, Shaheerah and Majidian, Sina and Malakar, Ayan and Mangolini, Tania Girão and Modha, Sejal and Moldes, Mauricio and Mondal, Rajarshi and Al Nahid, Abdullah and Poon, Chi-Lam and Sagayaradj, Sagayamary and Sanio, Philippe and Sepulveda-Morales, Tania and Shahzaib, Muhammad and Raza, Muhammad Sohail and Tat, Trinh and Thota, Ishaan and Yaman, Umran and Yeung, Jason and Yu, Qiyi and Zheng, Xinchang and Mahmoud, Medhat and Sedlazeck, Fritz J. and Busby, Ben}},
  issn         = {{2046-1402}},
  keywords     = {{Structural variants; RNA-seq; Metagenomics; Mosaicism; long-read sequencing; Hackathon; NGS}},
  language     = {{eng}},
  month        = {{06}},
  pages        = {{1--33}},
  publisher    = {{F1000 Research Ltd.}},
  series       = {{F1000Research}},
  title        = {{The fifth international hackathon for developing computational cloud-based tools and resources for pan-structural variation and genomics}},
  url          = {{http://dx.doi.org/10.12688/f1000research.148237.1}},
  doi          = {{10.12688/f1000research.148237.1}},
  volume       = {{13}},
  year         = {{2024}},
}