F1000Res . An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates

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F1000Res


. 2021 Mar 26;10:246.
doi: 10.12688/f1000research.51477.2. eCollection 2021.
An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates


Ann M Mc Cartney ¹ , Medhat Mahmoud ² , Michael Jochum ² , Daniel Paiva Agustinho ³ , Barry Zorman ² , Ahmad Al Khleifat ⁴ , Fawaz Dabbaghie ⁵ , Rupesh K Kesharwani ² , Moritz Smolka ⁶ , Moez Dawood ² , Dreycey Albin ⁷ , Elbay Aliyev ⁸ , Hakeem Almabrazi ⁸ , Ahmed Arslan ⁹ , Advait Balaji ¹⁰ , Sairam Behera ² , Kimberley Billingsley ¹ , Daniel L Cameron ¹¹ , Joyjit Daw ¹² , Eric T Dawson ¹² , Wouter De Coster ¹³ , Haowei Du ² , Christopher Dunn ¹⁴ , Rocio Esteban ¹⁵ , Angad Jolly ² , Divya Kalra ² , Chunxiao Liao ¹⁰ , Yunxi Liu ¹⁰ , Tsung-Yu Lu ¹⁶ , James M Havrilla ¹⁷ , Michael M Khayat ² , Maximillian Marin ¹⁸ , Jean Monlong ¹⁹ , Stephen Price ²⁰ , Alejandro Rafael Gener ² , Jingwen Ren ¹⁶ , Sagayamary Sagayaradj ²¹ , Nicolae Sapoval ¹⁰ , Claude Sinner ²² , Daniela C Soto ²¹ , Arda Soylev ²³ , Arun Subramaniyan ²⁴ , Najeeb Syed ⁸ , Neha Tadimeti ¹² , Pamella Tater ²⁵ , Pankaj Vats ¹² , Justin Vaughn ²⁶ , Kimberly Walker ² , Gaojianyong Wang ²⁷ , Qiandong Zeng ²⁸ , Shangzhe Zhang ²⁹ , Tingting Zhao ³⁰ , Bryce Kille ¹⁰ , Evan Biederstedt ¹⁸ , Mark Chaisson ¹⁶ , Adam English ² , Zev Kronenberg ¹⁴ , Todd J Treangen ¹⁰ , Timothy Hefferon ¹ , Chen-Shan Chin ²⁵ , Ben Busby ²⁵ , Fritz J Sedlazeck ²



Affiliations

• PMID: 34621504
• PMCID: PMC8479851
• DOI: 10.12688/f1000research.51477.2

Free PMC article

Abstract

In October 2020, 62 scientists from nine nations worked together remotely in the Second Baylor College of Medicine & DNAnexus hackathon, focusing on different related topics on Structural Variation, Pan-genomes, and SARS-CoV-2 related research. The overarching focus was to assess the current status of the field and identify the remaining challenges. Furthermore, how to combine the strengths of the different interests to drive research and method development forward. Over the four days, eight groups each designed and developed new open-source methods to improve the identification and analysis of variations among species, including humans and SARS-CoV-2. These included improvements in SV calling, genotyping, annotations and filtering. Together with advancements in benchmarking existing methods. Furthermore, groups focused on the diversity of SARS-CoV-2. Daily discussion summary and methods are available publicly at https://github.com/collaborativebioinformatics provides valuable insights for both participants and the research community.

Keywords: CNV; NextGeneration Sequencing; SARS-CoV-2; Structural variant.