Scoary protocols

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Scoary statistics

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Associated diseases

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Scoary specifications

Information


Unique identifier OMICS_13120
Name Scoary
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data The ‘gene_presence_absence’ file from Roary and a list of traits to test associations to.
Input format CSV
Output data A single list of significant genes per trait.
Output format CSV
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.6.16
Stability Stable
Requirements
Roary, SciPy
Source code URL https://codeload.github.com/AdmiralenOla/Scoary/zip/master
Maintained Yes

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Maintainer


  • person_outline Ola Brynildsrud <>

Publication for Scoary

Scoary in pipeline

2017
PMCID: 5451516
PMID: 28593194
DOI: 10.1128/mSphere.00168-17

[…] resistance was determined using rgi (https://card.mcmaster.ca/analyze/rgi) (). the presence of 40 virulence factor genes () was determined using a blast search (clc genomics workbench v9)., scoary () was used to identify genes found be present in virtually all members of a subgroup and rare or absent in all other subgroups. the resulting gene sets were then examined for genes likely […]


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Scoary in publications

 (11)
PMCID: 5885014
PMID: 29498619
DOI: 10.1099/mgen.0.000162

[…] novo assemblies were annotated using prokka [], and these were then used in the pan-genome analysis using roary []. a cut-off of 95 % was used to define the locus match in the pan-genome analysis. scoary [], with 50 permutation tests for the empirical p-value, was used to identify accessory genes in isolates from wastewater versus clinical origin. after reconstruction of the core genome […]

PMCID: 5828338
PMID: 29482512
DOI: 10.1186/s12866-018-1160-5

[…] the genetic repertoire of each isolate was analysed using roary [], and finally potential correlations between disease cohort and genetic content examined for statistical significance with scoary []. p-values were adjusted using the bonferroni correction method., the binding assay was performed as previously described [, ], with some modifications. human fibronectin (fibrp-ro roche, […]

PMCID: 5784243
PMID: 29404412
DOI: 10.1128/mSphere.00517-17

[…] were determined for the six sequenced isolates (). the pan-genome of the six isolates comprised 7,537 genes; of these, 3,502 genes were common to all isolates and constituted the core genome. scoary analysis to determine if genes were significantly associated with the three etec-only infections did not reveal any significant results. the only differences found were larger genomes […]

PMCID: 5744393
PMID: 29282103
DOI: 10.1186/s13073-017-0507-0

[…] were annotated with prokka [], and the output used to reconstruct the pan-genome using roary []. a core genome was created for each isolate using a 99% cut-off, with a default 95% identity cut-off. scoary [] was used with 50 re-samplings in the permutation test to find significant associations between the presence and absence of genes in the pan-genome and antibiotic susceptible/resistant […]

PMCID: 5705806
PMID: 29202045
DOI: 10.1128/mSphere.00511-17

[…] gene content among the members of this larger sample of isolates, we decided to test for relative differences in accessory gene content between human clinical isolates and other isolates using scoary (), which performs a genome-wide association study (gwas) using gene presence and absence. we did not identify any genes that were significantly associated with the human-pathogenic niche […]


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Scoary institution(s)
Domain of Infectious Disease Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway; Hanze University of Applied Sciences, Groningen, The Netherlands
Scoary funding source(s)
Supported by the Norwegian Institute of Public Health (NIPH) and a postdoctoral fellowship from the Norwegian Research Council (Grant 221562).

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