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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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Documentation


Maintainer


  • person_outline Ola Brynildsrud

Publication for Scoary

Scoary citations

 (12)
library_books

Piggy: a rapid, large scale pan genome analysis tool for intergenic regions in bacteria

2018
GigaScience
PMCID: 5890482
PMID: 29635296
DOI: 10.1093/gigascience/giy015

[…] sence.csv” file produced by Roary and can be loaded directly into the interactive browser-based viewer Phandango [] (Supplementary Fig. S2). It can also be used as input, along with a traits file, to Scoary [] to test for associations between IGRs and phenotypic traits. Moreover, the “representative_clusters_merged.fasta” file can be loaded directly into BIGSdb [] to create an allele scheme for IG […]

library_books

Genomic survey of Clostridium difficile reservoirs in the East of England implicates environmental contamination of wastewater treatment plants by clinical lineages

2018
Microb Genom
PMCID: 5885014
PMID: 29498619
DOI: 10.1099/mgen.0.000162

[…] de 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 alignme […]

library_books

Exploring the arthritogenicity of Streptococcus dysgalactiae subspecies equisimilis

2018
BMC Microbiol
PMCID: 5828338
PMID: 29482512
DOI: 10.1186/s12866-018-1160-5

[…] bsequently 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. […]

library_books

In Situ Analyses Directly in Diarrheal Stool Reveal Large Variations in Bacterial Load and Active Toxin Expression of Enterotoxigenic Escherichia coli and Vibrio cholerae

2018
PMCID: 5784243
PMID: 29404412
DOI: 10.1128/mSphere.00517-17

[…] and no consensus regarding the CF/toxin profiles and disease outcome has been determined to date ().Next, we sought to determine why certain ETEC toxin-CF combinations manifest as single infections. Scoary analysis of the genomes, however, did not reveal any unique gene profiles that could explain the single-pathogen infections seen for samples 4, 5, and 18. Analysis of antibiotic resistance gene […]

library_books

Within host evolution of Enterococcus faecium during longitudinal carriage and transition to bloodstream infection in immunocompromised patients

2017
Genome Med
PMCID: 5744393
PMID: 29282103
DOI: 10.1186/s13073-017-0507-0

[…] h 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 and ca […]

library_books

Adaptation in a Fibronectin Binding Autolysin of Staphylococcus saprophyticus

2017
PMCID: 5705806
PMID: 29202045
DOI: 10.1128/mSphere.00511-17

[…] mblies using Prokka v 1.11 () and used Roary () to identify orthologous genes in the core and accessory genomes. To look for associations between accessory gene content and human association, we used Scoary (). For the analysis, we used human association as the trait of interest, and we adjusted the P value for multiple comparisons using the Bonferroni method. […]

Citations

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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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