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GAGE specifications

Information


Unique identifier OMICS_14893
Name GAGE
Alternative name Genome Assembly Gold-standard Evaluations
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Documentation


Maintainer


  • person_outline Steven Salzberg

Publications for Genome Assembly Gold-standard Evaluations

GAGE citations

 (4)
library_books

Reference guided de novo assembly approach improves genome reconstruction for related species

2017
BMC Bioinformatics
PMCID: 5681816
PMID: 29126390
DOI: 10.1186/s12859-017-1911-6

[…] [] to calculate the size of an average A. lyrata gene. We also estimated the NG50 (length of the contigs that using equal or longer contigs sum up to half of the A. lyrata genome length []) using the genome assembly gold-standard evaluations tool GAGE []. Additionally, the number of misassemblies (translocations: number of sequences in a contig/scaffold which map on different reference chromosomes […]

library_books

Finishing monkeypox genomes from short reads: assembly analysis and a neural network method

2016
BMC Genomics
PMCID: 5009526
PMID: 27585810
DOI: 10.1186/s12864-016-2826-8

[…] cal and theoretical motives have served to put pathogen genomic sequencing high on the priority lists of public health agencies, such as the CDC.A definition of “high-quality” has been promulgated by Genome Assembly Gold-Standard Evaluations (GAGE) [, ] and applied in two competitions for quality assembly: “Assemblathon” [, ] and the “De Novo Genome Assembly Assessment Project” (dnGASP) []. These […]

library_books

Identification of Optimum Sequencing Depth Especially for De Novo Genome Assembly of Small Genomes Using Next Generation Sequencing Data

2013
PLoS One
PMCID: 3625192
PMID: 23593174
DOI: 10.1371/journal.pone.0060204

[…] The assembly validation script designed for the GAGE (Genome Assembly Gold-Standard Evaluations) assembly comparison project was used to evaluate the validity of the assemblies produced in this study. The assembly validation scripts make use of MUMmer […]

library_books

Beginner’s guide to comparative bacterial genome analysis using next generation sequence data

2013
Microb Inform Exp
PMCID: 3630013
PMID: 23575213
DOI: 10.1186/2042-5783-3-2

[…] ts such as prophages, and the very nature of short-read assemblers, there will almost certainly be assembly errors present within the contigs. Indeed, all assemblers used in Assemblathon 1 [] and the Genome Assembly Gold-standard Evaluations (GAGE) [] community “bake-offs” produced assemblies with errors. The error rate of an assembly can be assessed if a closely related reference genome is availa […]

Citations

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GAGE institution(s)
McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; National Biodefense Analysis and Countermeasures Center, Battelle National Biodefense Institute, Frederick, MD, USA; Institute for Physical Sciences and Technology, University of Maryland, College Park, MD, USA; Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA; Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA; Division for Bioinformatics, Innsbruck Medical University, Innsbruck, Austria
GAGE funding source(s)
This work was supported in part by the U.S. National Institute of Health under grants R01-HG006677 and R01-HG006102, and the USDA's National Institute of Food and Agriculture (NIFA) under grants 2009-35205-05209 and 2011-67009-30030.

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