Future-Proofing Your Microbiology Resource Announcements Genome Assembly for Reproducibility and Clarity
Abstract
Descriptions of resources, like the genome assemblies reported in Microbiology Resource Announcements, are often frozen at their time of publication, yet they will need to be interpreted in the midst of continually evolving technologies. It is therefore important to ensure that researchers accessing published resources have access to all of the information required to repeat, interpret, and extend these original analyses. Here, we provide a set of suggestions to help make certain that published resources remain useful and repeatable for the foreseeable future.
- Authors:
-
[1];
[2];
[5];
[4];
[7];
[8];
[9]
- Univ. of Arizona, Tucson, AZ (United States)
- Broad Inst. of MIT and Harvard, Cambridge, MA (United States)
- Queens College of the City Univ. of New York, Queens, NY (United States); The Graduate Center of The City Univ. of New York, New York, NY (United States)
- Univ. of Maryland, Baltimore, MD (United States)
- Univ. of Delaware, Newark, DE (United States)
- Indiana Univ., Bloomington, IN (United States)
- Vanderbilt Univ., Nashville, TN (United States)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- Univ. of California, Riverside, CA (United States)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1581365
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Microbiology Resource Announcements
- Additional Journal Information:
- Journal Volume: 8; Journal Issue: 36; Journal ID: ISSN 2576-098X
- Publisher:
- SSPA - American Society for Microbiology
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Baltrus, David A., Cuomo, Christina A., Dennehy, John J., Dunning Hotopp, Julie C., Maresca, Julia A., Newton, Irene L. G., Rasko, David A., Rokas, Antonis, Roux, Simon, and Stajich, Jason E. Future-Proofing Your Microbiology Resource Announcements Genome Assembly for Reproducibility and Clarity. United States: N. p., 2019.
Web. doi:10.1128/MRA.00954-19.
Baltrus, David A., Cuomo, Christina A., Dennehy, John J., Dunning Hotopp, Julie C., Maresca, Julia A., Newton, Irene L. G., Rasko, David A., Rokas, Antonis, Roux, Simon, & Stajich, Jason E. Future-Proofing Your Microbiology Resource Announcements Genome Assembly for Reproducibility and Clarity. United States. https://doi.org/10.1128/MRA.00954-19
Baltrus, David A., Cuomo, Christina A., Dennehy, John J., Dunning Hotopp, Julie C., Maresca, Julia A., Newton, Irene L. G., Rasko, David A., Rokas, Antonis, Roux, Simon, and Stajich, Jason E. Thu .
"Future-Proofing Your Microbiology Resource Announcements Genome Assembly for Reproducibility and Clarity". United States. https://doi.org/10.1128/MRA.00954-19. https://www.osti.gov/servlets/purl/1581365.
@article{osti_1581365,
title = {Future-Proofing Your Microbiology Resource Announcements Genome Assembly for Reproducibility and Clarity},
author = {Baltrus, David A. and Cuomo, Christina A. and Dennehy, John J. and Dunning Hotopp, Julie C. and Maresca, Julia A. and Newton, Irene L. G. and Rasko, David A. and Rokas, Antonis and Roux, Simon and Stajich, Jason E.},
abstractNote = {Descriptions of resources, like the genome assemblies reported in Microbiology Resource Announcements, are often frozen at their time of publication, yet they will need to be interpreted in the midst of continually evolving technologies. It is therefore important to ensure that researchers accessing published resources have access to all of the information required to repeat, interpret, and extend these original analyses. Here, we provide a set of suggestions to help make certain that published resources remain useful and repeatable for the foreseeable future.},
doi = {10.1128/MRA.00954-19},
journal = {Microbiology Resource Announcements},
number = 36,
volume = 8,
place = {United States},
year = {2019},
month = {9}
}
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Works referenced in this record:
The minimum information about a genome sequence (MIGS) specification
journal, May 2008
- Field, Dawn; Garrity, George; Gray, Tanya
- Nature Biotechnology, Vol. 26, Issue 5
Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
journal, November 2014
- Walker, Bruce J.; Abeel, Thomas; Shea, Terrance
- PLoS ONE, Vol. 9, Issue 11
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications
journal, May 2011
- Yilmaz, Pelin; Kottmann, Renzo; Field, Dawn
- Nature Biotechnology, Vol. 29, Issue 5
Reproducible big data science: A case study in continuous FAIRness
journal, April 2019
- Madduri, Ravi; Chard, Kyle; D’Arcy, Mike
- PLOS ONE, Vol. 14, Issue 4
Measuring the reproducibility and quality of Hi-C data
journal, March 2019
- Yardımcı, Galip Gürkan; Ozadam, Hakan; Sauria, Michael E. G.
- Genome Biology, Vol. 20, Issue 1
Genome Diversity of Pseudomonas aeruginosa PAO1 Laboratory Strains
journal, December 2009
- Klockgether, J.; Munder, A.; Neugebauer, J.
- Journal of Bacteriology, Vol. 192, Issue 4, p. 1113-1121
Computational and Informatic Advances for Reproducible Data Analysis in Neuroimaging
journal, July 2019
- Poldrack, Russell A.; Gorgolewski, Krzysztof J.; Varoquaux, Gaël
- Annual Review of Biomedical Data Science, Vol. 2, Issue 1
Genomic Plasticity Enables Phenotypic Variation of Pseudomonas syringae pv. tomato DC3000
journal, February 2014
- Bao, Zhongmeng; Stodghill, Paul V.; Myers, Christopher R.
- PLoS ONE, Vol. 9, Issue 2
The Genome-Sequenced Variant of Campylobacter jejuni NCTC 11168 and the Original Clonal Clinical Isolate Differ Markedly in Colonization, Gene Expression, and Virulence-Associated Phenotypes
journal, December 2003
- Gaynor, E. C.; Cawthraw, S.; Manning, G.
- Journal of Bacteriology, Vol. 186, Issue 2
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
journal, August 2017
- Bowers, Robert M.; Kyrpides, Nikos C.; Stepanauskas, Ramunas
- Nature Biotechnology, Vol. 35, Issue 8
Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads
journal, June 2017
- Wick, Ryan R.; Judd, Louise M.; Gorrie, Claire L.
- PLOS Computational Biology, Vol. 13, Issue 6
Reproducible Big Data Science: A Case Study In Continuous Fairness
text, January 2018
- Chard, Kyle; Madduri, Ravi; D'Arcy, Michael
- Zenodo
The Genome-Sequenced Variant of Campylobacter jejuni NCTC 11168 and the Original Clonal Clinical Isolate Differ Markedly in Colonization, Gene Expression, and Virulence-Associated Phenotypes
journal, December 2004
- Gaynor, Erin C.; Cawthraw, Shaun; Manning, Georgina
- Journal of Bacteriology, Vol. 186, Issue 23
Reproducible Big Data Science: A Case Study In Continuous Fairness
text, January 2018
- Chard, Kyle; Madduri, Ravi; D'Arcy, Michael
- Zenodo