tetano
Editor, Senior Moderator
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[SUP] 1 [/SUP], Medhat Mahmoud[SUP] 2 [/SUP], Michael Jochum[SUP] 2 [/SUP], Daniel Paiva Agustinho[SUP] 3 [/SUP], Barry Zorman[SUP] 2 [/SUP], Ahmad Al Khleifat[SUP] 4 [/SUP], Fawaz Dabbaghie[SUP] 5 [/SUP], Rupesh K Kesharwani[SUP] 2 [/SUP], Moritz Smolka[SUP] 6 [/SUP], Moez Dawood[SUP] 2 [/SUP], Dreycey Albin[SUP] 7 [/SUP], Elbay Aliyev[SUP] 8 [/SUP], Hakeem Almabrazi[SUP] 8 [/SUP], Ahmed Arslan[SUP] 9 [/SUP], Advait Balaji[SUP] 10 [/SUP], Sairam Behera[SUP] 2 [/SUP], Kimberley Billingsley[SUP] 1 [/SUP], Daniel L Cameron[SUP] 11 [/SUP], Joyjit Daw[SUP] 12 [/SUP], Eric T Dawson[SUP] 12 [/SUP], Wouter De Coster[SUP] 13 [/SUP], Haowei Du[SUP] 2 [/SUP], Christopher Dunn[SUP] 14 [/SUP], Rocio Esteban[SUP] 15 [/SUP], Angad Jolly[SUP] 2 [/SUP], Divya Kalra[SUP] 2 [/SUP], Chunxiao Liao[SUP] 10 [/SUP], Yunxi Liu[SUP] 10 [/SUP], Tsung-Yu Lu[SUP] 16 [/SUP], James M Havrilla[SUP] 17 [/SUP], Michael M Khayat[SUP] 2 [/SUP], Maximillian Marin[SUP] 18 [/SUP], Jean Monlong[SUP] 19 [/SUP], Stephen Price[SUP] 20 [/SUP], Alejandro Rafael Gener[SUP] 2 [/SUP], Jingwen Ren[SUP] 16 [/SUP], Sagayamary Sagayaradj[SUP] 21 [/SUP], Nicolae Sapoval[SUP] 10 [/SUP], Claude Sinner[SUP] 22 [/SUP], Daniela C Soto[SUP] 21 [/SUP], Arda Soylev[SUP] 23 [/SUP], Arun Subramaniyan[SUP] 24 [/SUP], Najeeb Syed[SUP] 8 [/SUP], Neha Tadimeti[SUP] 12 [/SUP], Pamella Tater[SUP] 25 [/SUP], Pankaj Vats[SUP] 12 [/SUP], Justin Vaughn[SUP] 26 [/SUP], Kimberly Walker[SUP] 2 [/SUP], Gaojianyong Wang[SUP] 27 [/SUP], Qiandong Zeng[SUP] 28 [/SUP], Shangzhe Zhang[SUP] 29 [/SUP], Tingting Zhao[SUP] 30 [/SUP], Bryce Kille[SUP] 10 [/SUP], Evan Biederstedt[SUP] 18 [/SUP], Mark Chaisson[SUP] 16 [/SUP], Adam English[SUP] 2 [/SUP], Zev Kronenberg[SUP] 14 [/SUP], Todd J Treangen[SUP] 10 [/SUP], Timothy Hefferon[SUP] 1 [/SUP], Chen-Shan Chin[SUP] 25 [/SUP], Ben Busby[SUP] 25 [/SUP], Fritz J Sedlazeck[SUP] 2 [/SUP]
Affiliations
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.
. 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[SUP] 1 [/SUP], Medhat Mahmoud[SUP] 2 [/SUP], Michael Jochum[SUP] 2 [/SUP], Daniel Paiva Agustinho[SUP] 3 [/SUP], Barry Zorman[SUP] 2 [/SUP], Ahmad Al Khleifat[SUP] 4 [/SUP], Fawaz Dabbaghie[SUP] 5 [/SUP], Rupesh K Kesharwani[SUP] 2 [/SUP], Moritz Smolka[SUP] 6 [/SUP], Moez Dawood[SUP] 2 [/SUP], Dreycey Albin[SUP] 7 [/SUP], Elbay Aliyev[SUP] 8 [/SUP], Hakeem Almabrazi[SUP] 8 [/SUP], Ahmed Arslan[SUP] 9 [/SUP], Advait Balaji[SUP] 10 [/SUP], Sairam Behera[SUP] 2 [/SUP], Kimberley Billingsley[SUP] 1 [/SUP], Daniel L Cameron[SUP] 11 [/SUP], Joyjit Daw[SUP] 12 [/SUP], Eric T Dawson[SUP] 12 [/SUP], Wouter De Coster[SUP] 13 [/SUP], Haowei Du[SUP] 2 [/SUP], Christopher Dunn[SUP] 14 [/SUP], Rocio Esteban[SUP] 15 [/SUP], Angad Jolly[SUP] 2 [/SUP], Divya Kalra[SUP] 2 [/SUP], Chunxiao Liao[SUP] 10 [/SUP], Yunxi Liu[SUP] 10 [/SUP], Tsung-Yu Lu[SUP] 16 [/SUP], James M Havrilla[SUP] 17 [/SUP], Michael M Khayat[SUP] 2 [/SUP], Maximillian Marin[SUP] 18 [/SUP], Jean Monlong[SUP] 19 [/SUP], Stephen Price[SUP] 20 [/SUP], Alejandro Rafael Gener[SUP] 2 [/SUP], Jingwen Ren[SUP] 16 [/SUP], Sagayamary Sagayaradj[SUP] 21 [/SUP], Nicolae Sapoval[SUP] 10 [/SUP], Claude Sinner[SUP] 22 [/SUP], Daniela C Soto[SUP] 21 [/SUP], Arda Soylev[SUP] 23 [/SUP], Arun Subramaniyan[SUP] 24 [/SUP], Najeeb Syed[SUP] 8 [/SUP], Neha Tadimeti[SUP] 12 [/SUP], Pamella Tater[SUP] 25 [/SUP], Pankaj Vats[SUP] 12 [/SUP], Justin Vaughn[SUP] 26 [/SUP], Kimberly Walker[SUP] 2 [/SUP], Gaojianyong Wang[SUP] 27 [/SUP], Qiandong Zeng[SUP] 28 [/SUP], Shangzhe Zhang[SUP] 29 [/SUP], Tingting Zhao[SUP] 30 [/SUP], Bryce Kille[SUP] 10 [/SUP], Evan Biederstedt[SUP] 18 [/SUP], Mark Chaisson[SUP] 16 [/SUP], Adam English[SUP] 2 [/SUP], Zev Kronenberg[SUP] 14 [/SUP], Todd J Treangen[SUP] 10 [/SUP], Timothy Hefferon[SUP] 1 [/SUP], Chen-Shan Chin[SUP] 25 [/SUP], Ben Busby[SUP] 25 [/SUP], Fritz J Sedlazeck[SUP] 2 [/SUP]
Affiliations
- PMID: 34621504
- PMCID: PMC8479851
- DOI: 10.12688/f1000research.51477.2
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.