B
Brett T. Hannigan
Publications - 5
Citations - 1266
Brett T. Hannigan is an academic researcher. The author has contributed to research in topics: Genome & Genomics. The author has an hindex of 5, co-authored 5 publications receiving 235 citations.
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Journal ArticleDOI
Towards complete and error-free genome assemblies of all vertebrate species
Arang Rhie,Shane A. McCarthy,Shane A. McCarthy,Olivier Fedrigo,Joana Damas,Giulio Formenti,Sergey Koren,Marcela Uliano-Silva,William Chow,Arkarachai Fungtammasan,J. H. Kim,Chul Hee Lee,Byung June Ko,Mark Chaisson,Gregory Gedman,Lindsey J. Cantin,Françoise Thibaud-Nissen,Leanne Haggerty,Iliana Bista,Iliana Bista,Michelle Smith,Bettina Haase,Jacquelyn Mountcastle,Sylke Winkler,Sylke Winkler,Sadye Paez,Jason T. Howard,Sonja C. Vernes,Sonja C. Vernes,Sonja C. Vernes,Tanya M. Lama,Frank Grützner,Wesley C. Warren,Christopher N. Balakrishnan,Dave W Burt,Jimin George,Matthew T. Biegler,David Iorns,Andrew Digby,Daryl Eason,Bruce C. Robertson,Taylor Edwards,Mark Wilkinson,George F. Turner,Axel Meyer,Andreas F. Kautt,Andreas F. Kautt,Paolo Franchini,H. William Detrich,Hannes Svardal,Hannes Svardal,Maximilian Wagner,Gavin J. P. Naylor,Martin Pippel,Milan Malinsky,Milan Malinsky,Mark Mooney,Maria Simbirsky,Brett T. Hannigan,Trevor Pesout,Marlys L. Houck,Ann C Misuraca,Sarah B. Kingan,Richard Hall,Zev N. Kronenberg,Ivan Sović,Christopher Dunn,Zemin Ning,Alex Hastie,Joyce V. Lee,Siddarth Selvaraj,Richard E. Green,Nicholas H. Putnam,Ivo Gut,Jay Ghurye,Erik Garrison,Ying Sims,Joanna Collins,Sarah Pelan,James Torrance,Alan Tracey,Jonathan Wood,Robel E. Dagnew,Dengfeng Guan,Dengfeng Guan,Sarah E. London,David F. Clayton,Claudio V. Mello,Samantha R. Friedrich,Peter V. Lovell,Ekaterina Osipova,Farooq O. Al-Ajli,Farooq O. Al-Ajli,Simona Secomandi,Heebal Kim,Constantina Theofanopoulou,Michael Hiller,Yang Zhou,Robert S. Harris,Kateryna D. Makova,Paul Medvedev,Jinna Hoffman,Patrick Masterson,Karen Clark,Fergal J. Martin,Kevin L. Howe,Paul Flicek,Brian P. Walenz,Woori Kwak,Hiram Clawson,Mark Diekhans,Luis R Nassar,Benedict Paten,Robert H. S. Kraus,Robert H. S. Kraus,Andrew J. Crawford,M. Thomas P. Gilbert,M. Thomas P. Gilbert,Guojie Zhang,Byrappa Venkatesh,Robert W. Murphy,Klaus-Peter Koepfli,Beth Shapiro,Beth Shapiro,Warren E. Johnson,Warren E. Johnson,Federica Di Palma,Tomas Marques-Bonet,Emma C. Teeling,Tandy Warnow,Jennifer A. Marshall Graves,Oliver A. Ryder,Oliver A. Ryder,David Haussler,Stephen J. O'Brien,Jonas Korlach,Harris A. Lewin,Kerstin Howe,Eugene W. Myers,Eugene W. Myers,Richard Durbin,Richard Durbin,Adam M. Phillippy,Erich D. Jarvis,Erich D. Jarvis +144 more
TL;DR: The Vertebrate Genomes Project (VGP) as mentioned in this paper is an international effort to generate high quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.
Posted ContentDOI
Towards complete and error-free genome assemblies of all vertebrate species
Arang Rhie,Shane A. McCarthy,Olivier Fedrigo,Joana Damas,Giulio Formenti,Sergey Koren,Marcela Uliano-Silva,William Chow,Arkarachai Fungtammasan,Gregory Gedman,Lindsey J. Cantin,Françoise Thibaud-Nissen,Leanne Haggerty,Chul Hee Lee,Byung June Ko,J. H. Kim,Iliana Bista,Michelle Smith,Bettina Haase,Jacquelyn Mountcastle,Sylke Winkler,Sadye Paez,Jason T. Howard,Sonja C. Vernes,Tanya M. Lama,Frank Grützner,Wesley C. Warren,Christopher N. Balakrishnan,Dave W Burt,Jimin George,Matthew T. Biegler,David Iorns,Andrew Digby,Daryl Eason,Taylor Edwards,Mark Wilkinson,George F. Turner,Axel Meyer,Andreas F. Kautt,Paolo Franchini,H. William Detrich,Hannes Svardal,Maximilian Wagner,Gavin J. P. Naylor,Martin Pippel,Milan Malinsky,Mark Mooney,Maria Simbirsky,Brett T. Hannigan,Trevor Pesout,Marlys L. Houck,Ann C Misuraca,Sarah B. Kingan,Richard Hall,Zev N. Kronenberg,Jonas Korlach,Ivan Sović,Christopher Dunn,Zemin Ning,Alex Hastie,Joyce V. Lee,Siddarth Selvaraj,Richard E. Green,Nicholas H. Putnam,Jay Ghurye,Erik Garrison,Ying Sims,Joanna Collins,Sarah Pelan,James Torrance,Alan Tracey,Jonathan Wood,Dengfeng Guan,Sarah E. London,David F. Clayton,Claudio V. Mello,Samantha R. Friedrich,Peter V. Lovell,Ekaterina Osipova,Farooq O. Al-Ajli,Simona Secomandi,Heebal Kim,Constantina Theofanopoulou,Yang Zhou,Robert S. Harris,Kateryna D. Makova,Paul Medvedev,Jinna Hoffman,Patrick Masterson,Karen Clark,Fergal J. Martin,Kevin L. Howe,Paul Flicek,Brian P. Walenz,Woori Kwak,Hiram Clawson,Mark Diekhans,Luis R Nassar,Benedict Paten,Robert H. S. Kraus,Harris A. Lewin,Andrew J. Crawford,M. Thomas P. Gilbert,Guojie Zhang,Byrappa Venkatesh,Robert W. Murphy,Klaus-Peter Koepfli,Beth Shapiro,Warren E. Johnson,Federica Di Palma,Tomas Marques-Bonet,Emma C. Teeling,Tandy Warnow,Jennifer A. Marshall Graves,Oliver A. Ryder,David Haussler,Stephen J. O'Brien,Kerstin Howe,Eugene W. Myers,Richard Durbin,Adam M. Phillippy,Erich D. Jarvis +121 more
TL;DR: The Vertebrate Genomes Project is embarked on, an effort to generate high-quality, complete reference genomes for all ~70,000 extant vertebrate species and help enable a new era of discovery across the life sciences.
Journal ArticleDOI
Effect of sequence depth and length in long-read assembly of the maize inbred NC358.
Shujun Ou,Jianing Liu,Kapeel Chougule,Arkarachai Fungtammasan,Arun S. Seetharam,Joshua C. Stein,Victor Llaca,Nancy Manchanda,Amanda M. Gilbert,Sharon Wei,Chen-Shan Chin,David E. Hufnagel,Sarah Pedersen,Samantha J. Snodgrass,Kevin Fengler,Margaret R. Woodhouse,Brian P. Walenz,Sergey Koren,Adam M. Phillippy,Brett T. Hannigan,R. Kelly Dawe,Candice N. Hirsch,Matthew B. Hufford,Doreen Ware,Doreen Ware +24 more
TL;DR: A set of PacBio reads is leveraged to develop guidelines for sequencing and assembly of complex plant genomes in order to allocate finite resources using maize as an example and shows high-quality optical maps can dramatically improve contiguity in even the most fragmented base assembly.
Posted ContentDOI
Effect of Sequence Depth and Length in Long-read Assembly of the Maize Inbred NC358
Shujun Ou,Jianing Liu,Kapeel Chougule,Arkarachai Fungtammasan,Arun S. Seetharam,Joshua C. Stein,Victor Llaca,Nancy Manchanda,Amanda M. Gilbert,Xuehong Wei,Chen-Shan Chin,David E. Hufnagel,Sarah Pedersen,Samantha J. Snodgrass,Kevin Fengler,Margaret R. Woodhouse,Brian P. Walenz,Sergey Koren,Adam M. Phillippy,Brett T. Hannigan,R. Kelly Dawe,Candice N. Hirsch,Matthew B. Hufford,Doreen Ware,Doreen Ware +24 more
TL;DR: This study generated eight independent assemblies for the complex genome of the maize inbred line NC358 using PacBio datasets ranging from 20-75x genomic depth and N50 read lengths of 11-21 kb, and distinguished sequence-quality thresholds were observed for complete assembly of genes, transposable elements, and highly repetitive genomic features.
Posted ContentDOI
How well can we create phased, diploid, human genomes?: An assessment of FALCON-Unzip phasing using a human trio
TL;DR: This research demonstrates that the FALCON-Unzip algorithm can be used to create long and accurate haplotypes for humans and identifies problematic regions that could benefit in future improvement.