Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy

Delphine Larivière; Linelle Abueg; Nadolina Brajuka; Cristóbal Gallardo-Alba; Bjorn Grüning; Byung June Ko; Alex Ostrovsky; Marc Palmada-Flores; Brandon D. Pickett; Keon Rabbani; Agostinho Antunes; Jennifer R. Balacco; Mark J.P. Chaisson; Haoyu Cheng; Joanna Collins; Melanie Couture; Alexandra Denisova; Olivier Fedrigo; Guido Roberto Gallo; Alice Maria Giani; Grenville Mac Donald Gooder; Kathleen Horan; Nivesh Jain; Cassidy Johnson; Heebal Kim; Chul Lee; Tomas Marques-Bonet; Brian O’Toole; Arang Rhie; Simona Secomandi; Marcella Sozzoni; Tatiana Tilley; Marcela Uliano-Silva; Marius van den Beek; Robert W. Williams; Robert M. Waterhouse; Adam M. Phillippy; Erich D. Jarvis; Michael C. Schatz; Anton Nekrutenko; Giulio Formenti

doi:10.1038/s41587-023-02100-3

Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy

Delphine Larivière
, Linelle Abueg
, Nadolina Brajuka
, Cristóbal Gallardo-Alba
, Bjorn Grüning
, Byung June Ko
, Alex Ostrovsky
, Marc Palmada-Flores
, Brandon D. Pickett
, Keon Rabbani
, Agostinho Antunes
, Jennifer R. Balacco
, Mark J.P. Chaisson
, Haoyu Cheng
, Joanna Collins
, Melanie Couture
, Alexandra Denisova
, Olivier Fedrigo
, Guido Roberto Gallo
, Alice Maria Giani

Grenville Mac Donald Gooder, Kathleen Horan, Nivesh Jain, Cassidy Johnson, Heebal Kim, Chul Lee, Tomas Marques-Bonet, Brian O’Toole, Arang Rhie, Simona Secomandi, Marcella Sozzoni, Tatiana Tilley, Marcela Uliano-Silva, Marius van den Beek, Robert W. Williams, Robert M. Waterhouse, Adam M. Phillippy, Erich D. Jarvis, Michael C. Schatz, Anton Nekrutenko, Giulio Formenti

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

41 Scopus citations

Original language	English (US)
Pages (from-to)	367-370
Number of pages	4
Journal	Nature Biotechnology
Volume	42
Issue number	3
DOIs	https://doi.org/10.1038/s41587-023-02100-3
State	Published - Mar 2024

All Science Journal Classification (ASJC) codes

Biotechnology
Bioengineering
Applied Microbiology and Biotechnology
Biomedical Engineering
Molecular Medicine

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10.1038/s41587-023-02100-3

Cite this

Larivière, D., Abueg, L., Brajuka, N., Gallardo-Alba, C., Grüning, B., Ko, B. J., Ostrovsky, A., Palmada-Flores, M., Pickett, B. D., Rabbani, K., Antunes, A., Balacco, J. R., Chaisson, M. J. P., Cheng, H., Collins, J., Couture, M., Denisova, A., Fedrigo, O., Gallo, G. R., ... Formenti, G. (2024). Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy. Nature Biotechnology, 42(3), 367-370. https://doi.org/10.1038/s41587-023-02100-3

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title = "Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy",

author = "Delphine Larivi{\`e}re and Linelle Abueg and Nadolina Brajuka and Crist{\'o}bal Gallardo-Alba and Bjorn Gr{\"u}ning and Ko, \{Byung June\} and Alex Ostrovsky and Marc Palmada-Flores and Pickett, \{Brandon D.\} and Keon Rabbani and Agostinho Antunes and Balacco, \{Jennifer R.\} and Chaisson, \{Mark J.P.\} and Haoyu Cheng and Joanna Collins and Melanie Couture and Alexandra Denisova and Olivier Fedrigo and Gallo, \{Guido Roberto\} and Giani, \{Alice Maria\} and Gooder, \{Grenville Mac Donald\} and Kathleen Horan and Nivesh Jain and Cassidy Johnson and Heebal Kim and Chul Lee and Tomas Marques-Bonet and Brian O{\textquoteright}Toole and Arang Rhie and Simona Secomandi and Marcella Sozzoni and Tatiana Tilley and Marcela Uliano-Silva and \{van den Beek\}, Marius and Williams, \{Robert W.\} and Waterhouse, \{Robert M.\} and Phillippy, \{Adam M.\} and Jarvis, \{Erich D.\} and Schatz, \{Michael C.\} and Anton Nekrutenko and Giulio Formenti",

year = "2024",

month = mar,

doi = "10.1038/s41587-023-02100-3",

language = "English (US)",

volume = "42",

pages = "367--370",

journal = "Nature Biotechnology",

issn = "1087-0156",

publisher = "Nature Research",

number = "3",

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Larivière, D, Abueg, L, Brajuka, N, Gallardo-Alba, C, Grüning, B, Ko, BJ, Ostrovsky, A, Palmada-Flores, M, Pickett, BD, Rabbani, K, Antunes, A, Balacco, JR, Chaisson, MJP, Cheng, H, Collins, J, Couture, M, Denisova, A, Fedrigo, O, Gallo, GR, Giani, AM, Gooder, GMD, Horan, K, Jain, N, Johnson, C, Kim, H, Lee, C, Marques-Bonet, T, O’Toole, B, Rhie, A, Secomandi, S, Sozzoni, M, Tilley, T, Uliano-Silva, M, van den Beek, M, Williams, RW, Waterhouse, RM, Phillippy, AM, Jarvis, ED, Schatz, MC, Nekrutenko, A & Formenti, G 2024, 'Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy', Nature Biotechnology, vol. 42, no. 3, pp. 367-370. https://doi.org/10.1038/s41587-023-02100-3

TY - JOUR

T1 - Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy

AU - Larivière, Delphine

AU - Abueg, Linelle

AU - Brajuka, Nadolina

AU - Gallardo-Alba, Cristóbal

AU - Grüning, Bjorn

AU - Ko, Byung June

AU - Ostrovsky, Alex

AU - Palmada-Flores, Marc

AU - Pickett, Brandon D.

AU - Rabbani, Keon

AU - Antunes, Agostinho

AU - Balacco, Jennifer R.

AU - Chaisson, Mark J.P.

AU - Cheng, Haoyu

AU - Collins, Joanna

AU - Couture, Melanie

AU - Denisova, Alexandra

AU - Fedrigo, Olivier

AU - Gallo, Guido Roberto

AU - Giani, Alice Maria

AU - Gooder, Grenville Mac Donald

AU - Horan, Kathleen

AU - Jain, Nivesh

AU - Johnson, Cassidy

AU - Kim, Heebal

AU - Lee, Chul

AU - Marques-Bonet, Tomas

AU - O’Toole, Brian

AU - Rhie, Arang

AU - Secomandi, Simona

AU - Sozzoni, Marcella

AU - Tilley, Tatiana

AU - Uliano-Silva, Marcela

AU - van den Beek, Marius

AU - Williams, Robert W.

AU - Waterhouse, Robert M.

AU - Phillippy, Adam M.

AU - Jarvis, Erich D.

AU - Schatz, Michael C.

AU - Nekrutenko, Anton

AU - Formenti, Giulio

PY - 2024/3

Y1 - 2024/3

UR - https://www.scopus.com/pages/publications/85183389565

UR - https://www.scopus.com/pages/publications/85183389565#tab=citedBy

U2 - 10.1038/s41587-023-02100-3

DO - 10.1038/s41587-023-02100-3

M3 - Letter

C2 - 38278971

AN - SCOPUS:85183389565

SN - 1087-0156

VL - 42

SP - 367

EP - 370

JO - Nature Biotechnology

JF - Nature Biotechnology

IS - 3

ER -

Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy

All Science Journal Classification (ASJC) codes

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