The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms

Kimberly Walker; Divya Kalra; Rebecca Lowdon; Guangyi Chen; Fritz J. Sedlazeck; Ben Busby; David Molik; Daniela C. Soto; Fawaz Dabbaghie; Ahmad Al Khleifat; Medhat Mahmoud; Luis F. Paulin; Muhammad Sohail Raza; Susanne P. Pfeifer; Daniel Paiva Agustinho; Elbay Aliyev; Pavel Avdeyev; Enrico R. Barrozo; Sairam Behera; Kimberley Billingsley; Li Chuin Chong; Deepak Choubey; Wouter De Coster; Yilei Fu; Alejandro R. Gener; Timothy Hefferon; David Morgan Henke; Wolfram Höps; Anastasia Illarionova; Michael D. Jochum; Maria Jose; Rupesh K. Kesharwani; Sree Rohit Raj Kolora; Jedrzej Kubica; Priya Lakra; Damaris Lattimer; Chia Sin Liew; Bai Wei Lo; Chunhsuan Lo; Anneri Lötter; Sina Majidian; Suresh Kumar Mendem; Rajarshi Mondal; Hiroko Ohmiya; Nasrin Parvin; Carolina Peralta; Chi Lam Poon; Ramanandan Prabhakaran; Marie Saitou; Aditi Sammi; Philippe Sanio; Nicolae Sapoval; Najeeb Syed; Todd Treangen; Gaojianyong Wang; Tiancheng Xu; Jianzhi Yang; Shangzhe Zhang; Weiyu Zhou

doi:10.12688/f1000research.110194.1

The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms

Kimberly Walker, Divya Kalra, Rebecca Lowdon, Guangyi Chen, Fritz J. Sedlazeck, Ben Busby, David Molik, Daniela C. Soto, Fawaz Dabbaghie, Ahmad Al Khleifat, Medhat Mahmoud, Luis F. Paulin, Muhammad Sohail Raza, Susanne P. Pfeifer, Daniel Paiva Agustinho, Elbay Aliyev, Pavel Avdeyev, Enrico R. Barrozo, Sairam Behera, Kimberley BillingsleyLi Chuin Chong, Deepak Choubey, Wouter De Coster, Yilei Fu, Alejandro R. Gener, Timothy Hefferon, David Morgan Henke, Wolfram Höps, Anastasia Illarionova, Michael D. Jochum, Maria Jose, Rupesh K. Kesharwani, Sree Rohit Raj Kolora, Jedrzej Kubica, Priya Lakra, Damaris Lattimer, Chia Sin Liew, Bai Wei Lo, Chunhsuan Lo, Anneri Lötter, Sina Majidian, Suresh Kumar Mendem, Rajarshi Mondal, Hiroko Ohmiya, Nasrin Parvin, Carolina Peralta, Chi Lam Poon, Ramanandan Prabhakaran, Marie Saitou, Aditi Sammi, Philippe Sanio, Nicolae Sapoval, Najeeb Syed, Todd Treangen, Gaojianyong Wang, Tiancheng Xu, Jianzhi Yang, Shangzhe Zhang, Weiyu Zhou

Life Sciences, School of (SOLS)

Research output: Contribution to journal › Article › peer-review

1 Scopus citations

Abstract

In October 2021, 59 scientists from 14 countries and 13 U.S. states collaborated virtually in the Third Annual Baylor College of Medicine & DNANexus Structural Variation hackathon. The goal of the hackathon was to advance research on structural variants (SVs) by prototyping and iterating on open-source software. This led to nine hackathon projects focused on diverse genomics research interests, including various SV discovery and genotyping methods, SV sequence reconstruction, and clinically relevant structural variation, including SARS-CoV-2 variants. Repositories for the projects that participated in the hackathon are available at https://github.com/collaborativebioinformatics.

Original language	English (US)
Article number	530
Journal	F1000Research
Volume	11
DOIs	https://doi.org/10.12688/f1000research.110194.1
State	Published - 2022

Keywords

Cancer
Covid-19
Hackathon
K-mer
Long-reads
NGS
Structural variants
Tomatoes
Viral integration

ASJC Scopus subject areas

General Immunology and Microbiology
General Pharmacology, Toxicology and Pharmaceutics
General Biochemistry, Genetics and Molecular Biology

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10.12688/f1000research.110194.1

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Walker, K., Kalra, D., Lowdon, R., Chen, G., Sedlazeck, F. J., Busby, B., Molik, D., Soto, D. C., Dabbaghie, F., Khleifat, A. A., Mahmoud, M., Paulin, L. F., Raza, M. S., Pfeifer, S. P., Agustinho, D. P., Aliyev, E., Avdeyev, P., Barrozo, E. R., Behera, S., ... Zhou, W. (2022). The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms. F1000Research, 11, Article 530. https://doi.org/10.12688/f1000research.110194.1

Walker, K, Kalra, D, Lowdon, R, Chen, G, Sedlazeck, FJ, Busby, B, Molik, D, Soto, DC, Dabbaghie, F, Khleifat, AA, Mahmoud, M, Paulin, LF, Raza, MS, Pfeifer, SP, Agustinho, DP, Aliyev, E, Avdeyev, P, Barrozo, ER, Behera, S, Billingsley, K, Chong, LC, Choubey, D, De Coster, W, Fu, Y, Gener, AR, Hefferon, T, Henke, DM, Höps, W, Illarionova, A, Jochum, MD, Jose, M, Kesharwani, RK, Kolora, SRR, Kubica, J, Lakra, P, Lattimer, D, Liew, CS, Lo, BW, Lo, C, Lötter, A, Majidian, S, Mendem, SK, Mondal, R, Ohmiya, H, Parvin, N, Peralta, C, Poon, CL, Prabhakaran, R, Saitou, M, Sammi, A, Sanio, P, Sapoval, N, Syed, N, Treangen, T, Wang, G, Xu, T, Yang, J, Zhang, S & Zhou, W 2022, 'The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms', F1000Research, vol. 11, 530. https://doi.org/10.12688/f1000research.110194.1

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title = "The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms",

abstract = "In October 2021, 59 scientists from 14 countries and 13 U.S. states collaborated virtually in the Third Annual Baylor College of Medicine & DNANexus Structural Variation hackathon. The goal of the hackathon was to advance research on structural variants (SVs) by prototyping and iterating on open-source software. This led to nine hackathon projects focused on diverse genomics research interests, including various SV discovery and genotyping methods, SV sequence reconstruction, and clinically relevant structural variation, including SARS-CoV-2 variants. Repositories for the projects that participated in the hackathon are available at https://github.com/collaborativebioinformatics.",

keywords = "Cancer, Covid-19, Hackathon, K-mer, Long-reads, NGS, Structural variants, Tomatoes, Viral integration",

author = "Kimberly Walker and Divya Kalra and Rebecca Lowdon and Guangyi Chen and Sedlazeck, {Fritz J.} and Ben Busby and David Molik and Soto, {Daniela C.} and Fawaz Dabbaghie and Khleifat, {Ahmad Al} and Medhat Mahmoud and Paulin, {Luis F.} and Raza, {Muhammad Sohail} and Pfeifer, {Susanne P.} and Agustinho, {Daniel Paiva} and Elbay Aliyev and Pavel Avdeyev and Barrozo, {Enrico R.} and Sairam Behera and Kimberley Billingsley and Chong, {Li Chuin} and Deepak Choubey and {De Coster}, Wouter and Yilei Fu and Gener, {Alejandro R.} and Timothy Hefferon and Henke, {David Morgan} and Wolfram H{\"o}ps and Anastasia Illarionova and Jochum, {Michael D.} and Maria Jose and Kesharwani, {Rupesh K.} and Kolora, {Sree Rohit Raj} and Jedrzej Kubica and Priya Lakra and Damaris Lattimer and Liew, {Chia Sin} and Lo, {Bai Wei} and Chunhsuan Lo and Anneri L{\"o}tter and Sina Majidian and Mendem, {Suresh Kumar} and Rajarshi Mondal and Hiroko Ohmiya and Nasrin Parvin and Carolina Peralta and Poon, {Chi Lam} and Ramanandan Prabhakaran and Marie Saitou and Aditi Sammi and Philippe Sanio and Nicolae Sapoval and Najeeb Syed and Todd Treangen and Gaojianyong Wang and Tiancheng Xu and Jianzhi Yang and Shangzhe Zhang and Weiyu Zhou",

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doi = "10.12688/f1000research.110194.1",

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volume = "11",

journal = "F1000Research",

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AU - Walker, Kimberly

AU - Kalra, Divya

AU - Lowdon, Rebecca

AU - Chen, Guangyi

AU - Sedlazeck, Fritz J.

AU - Busby, Ben

AU - Molik, David

AU - Soto, Daniela C.

AU - Dabbaghie, Fawaz

AU - Khleifat, Ahmad Al

AU - Mahmoud, Medhat

AU - Paulin, Luis F.

AU - Raza, Muhammad Sohail

AU - Pfeifer, Susanne P.

AU - Agustinho, Daniel Paiva

AU - Aliyev, Elbay

AU - Avdeyev, Pavel

AU - Barrozo, Enrico R.

AU - Behera, Sairam

AU - Billingsley, Kimberley

AU - Chong, Li Chuin

AU - Choubey, Deepak

AU - De Coster, Wouter

AU - Fu, Yilei

AU - Gener, Alejandro R.

AU - Hefferon, Timothy

AU - Henke, David Morgan

AU - Höps, Wolfram

AU - Illarionova, Anastasia

AU - Jochum, Michael D.

AU - Jose, Maria

AU - Kesharwani, Rupesh K.

AU - Kolora, Sree Rohit Raj

AU - Kubica, Jedrzej

AU - Lakra, Priya

AU - Lattimer, Damaris

AU - Liew, Chia Sin

AU - Lo, Bai Wei

AU - Lo, Chunhsuan

AU - Lötter, Anneri

AU - Majidian, Sina

AU - Mendem, Suresh Kumar

AU - Mondal, Rajarshi

AU - Ohmiya, Hiroko

AU - Parvin, Nasrin

AU - Peralta, Carolina

AU - Poon, Chi Lam

AU - Prabhakaran, Ramanandan

AU - Saitou, Marie

AU - Sammi, Aditi

AU - Sanio, Philippe

AU - Sapoval, Nicolae

AU - Syed, Najeeb

AU - Treangen, Todd

AU - Wang, Gaojianyong

AU - Xu, Tiancheng

AU - Yang, Jianzhi

AU - Zhang, Shangzhe

AU - Zhou, Weiyu

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AB - In October 2021, 59 scientists from 14 countries and 13 U.S. states collaborated virtually in the Third Annual Baylor College of Medicine & DNANexus Structural Variation hackathon. The goal of the hackathon was to advance research on structural variants (SVs) by prototyping and iterating on open-source software. This led to nine hackathon projects focused on diverse genomics research interests, including various SV discovery and genotyping methods, SV sequence reconstruction, and clinically relevant structural variation, including SARS-CoV-2 variants. Repositories for the projects that participated in the hackathon are available at https://github.com/collaborativebioinformatics.

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KW - Covid-19

KW - Hackathon

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KW - Long-reads

KW - NGS

KW - Structural variants

KW - Tomatoes

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ER -

The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms

Abstract

Keywords

ASJC Scopus subject areas

Access to Document

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