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

Kascade-Grande Collaboration; Damaris Lattimer

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

Kascade-Grande Collaboration
, Damaris Lattimer

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

4 Citations (Scopus)

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
Article number	530
Pages (from-to)	530
Journal	F1000Research
Volume	11
DOIs	https://doi.org/10.12688/f1000research.110194.1
Publication status	Published - 2022

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Keywords

Cancer
Covid-19
Hackathon
K-mer
Long-reads
NGS
Structural variants
Tomatoes
Viral integration
SARS-CoV-2/genetics
Humans
Genomics
COVID-19
Software

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10.12688/f1000research.110194.1

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@article{61ae86fd96ee449b817bfa3602ca2969,

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, SARS-CoV-2/genetics, Humans, Genomics, COVID-19, Software",

author = "\{Kascade-Grande Collaboration\} and 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 Philippe Sanio",

note = "Funding Information: The hackathon was sponsored by Pacific Biosciences of California, Inc. and Oxford Nanopore Technologies Limited. We'd like to thank Richard Gibbs and the Baylor College of Medicine Human Genome Sequencing Center for hosting the hackathon. Computation was performed on the DNAnexus platform, which donated compute and storage to the hackathon. Publisher Copyright: {\textcopyright} 2022 Walker K et al..",

year = "2022",

doi = "10.12688/f1000research.110194.1",

language = "English",

volume = "11",

pages = "530",

journal = "F1000Research",

issn = "2046-1402",

publisher = "F1000 Research Ltd.",

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TY - JOUR

T1 - The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms

AU - Kascade-Grande Collaboration

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 - Sanio, Philippe

N1 - Funding Information: The hackathon was sponsored by Pacific Biosciences of California, Inc. and Oxford Nanopore Technologies Limited. We'd like to thank Richard Gibbs and the Baylor College of Medicine Human Genome Sequencing Center for hosting the hackathon. Computation was performed on the DNAnexus platform, which donated compute and storage to the hackathon. Publisher Copyright: © 2022 Walker K et al..

PY - 2022

Y1 - 2022

N2 - 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.

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.

KW - Cancer

KW - Covid-19

KW - Hackathon

KW - K-mer

KW - Long-reads

KW - NGS

KW - Structural variants

KW - Tomatoes

KW - Viral integration

KW - SARS-CoV-2/genetics

KW - Humans

KW - Genomics

KW - COVID-19

KW - Software

UR - https://www.scopus.com/pages/publications/85140214401

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DO - 10.12688/f1000research.110194.1

M3 - Article

C2 - 36262335

AN - SCOPUS:85140214401

SN - 2046-1402

VL - 11

SP - 530

JO - F1000Research

JF - F1000Research

M1 - 530

ER -

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

Abstract

UN SDGs

Keywords

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