Roary protocols

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Roary specifications

Information


Unique identifier OMICS_09491
Name Roary
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Annotated assemblies
Input format GFF3
Operating system Unix/Linux
Programming languages Perl
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Andrew J. Page <>

Publication for Roary

Roary in pipelines

 (37)
2018
PMCID: 5748942
PMID: 29291727
DOI: 10.1186/s12864-017-4249-6

[…] to compare the m. bovis strains from uruguay were downloaded from public databases, assembled with spades [], and annotated with prokka []. the pan genome of all the 186 strains was estimated with roary (v3.6.8) []; core genes were defined as those present in all 186 isolates with a 90% id cut-off. recombination was inspected using fastgear []. finally, core genes aligned with mafft [] […]

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

[…] whole-genome alignment was performed and visualized using progressivemauve v. 2015/2/25 (). pan-genome analysis was performed using roary v. 3.6.2 (), using a blastp identity cutoff of 85%. comparison between the etec-only infection genomes and mixed-infection genomes was performed using the scoary tool v. 1.6.10 ()., statistical […]

2018
PMCID: 5811526
PMID: 29479347
DOI: 10.3389/fmicb.2018.00188

[…] the analysis depicts current evolution of esbl-producing k. pneumoniae., phylogenetic analysis was based on the core genomes and performed using the rapid large-scale prokaryote pan genome analysis (roary) (). the maximum likelihood phylogenetic tree encompassing, country, population, sample type metadata and mlst type was generated, edited and visualized using fasttree version 2.1.7. […]

2018
PMCID: 5824051
PMID: 29237792
DOI: 10.1128/JCM.01384-17

[…] alignment using snp-sites (). a maximum likelihood tree based on snp alignment was constructed using fasttree with the settings -gamma and -gtr (), and the tree was visualized with itol ()., using roary analysis, c. difficile rt078 strains isolated from humans and animals with identical core genomes were extracted using an inhouse r script. ani was calculated by performing pairwise comparison […]

2018
PMCID: 5824064
PMID: 29263205
DOI: 10.1128/JCM.01520-17

[…] a qiaxtractor (qiagen), and sequencing was performed on an illumina hiseq 2000 instrument. sequence reads were assembled using velvet and annotated using prokka. the pangenome was estimated using roary () with a 98% identification (id) cutoff. the van gene in the two patients with genetically related vrefm and vsefm isolates was extracted from the roary pan genome and compared to the vana […]


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Roary in publications

 (113)
PMCID: 5944035
PMID: 29743119
DOI: 10.1186/s13062-018-0211-z

[…] asm59047v1, asm66191v1, asm95268v1, asm98286v1, asm103864v1, asm106422v1, asm127647v1, asm157508v1) which were first annotated using prokka [] and then clustered into gene-families with roary []. we profiled the 1572 new york samples from the metasub dataset with panphlan version 1.2.1.3., we defined the phylogenomic distance between two samples as the pairwise hamming distance […]

PMCID: 5932375
PMID: 29720528
DOI: 10.1128/mSphere.00571-17

[…] based on the seqtk toolkit (https://github.com/lh3/seqtk). antibiotic resistance phenotypes were predicted for each strain based on the methods of gordon et al. (). roary () was used to estimate a pan-genome from de novo-assembled contigs of the strains sequenced in the study. the mlst was ascertained using srst2 (). two strains were excluded because pangenome […]

PMCID: 5899146
PMID: 29654279
DOI: 10.1038/s41467-018-03949-8

[…] are used (and duly indicated)., in addition to the above, a combination of orthologue detection and mapping was used to infer pksr100 presence across all isolates. core genome analysis (using roary ref. ) of all uk representative subsample isolates and the msma s. flexneri 3a sublineage was used to identify the presence and count of 86 pksr100 orthologues among isolates. those isolates […]

PMCID: 5893538
PMID: 29636463
DOI: 10.1038/s41426-018-0065-6

[…] the core genome and the 23s rrna gene. the 23s rrna gene phylogenetic tree was generated using the maximum likelihood method implemented in mega6. the core genome phylogenetic tree was generated by roary., by comparing the draft genomes of 63 c. concisus strains generated using the miseq method, we found a genomic fragment that was only present in the draft genomes of strains p2cdo4, p20cdo-s2 […]

PMCID: 5902063
PMID: 29617440
DOI: 10.1371/journal.ppat.1006966

[…] was determined through a similar approach using srst2. de novo genome assemblies were generated with velvet [] and annotated using prokka v1.11 []. after annotation, the pangenome was analyzed with roary, and a concatenated alignment of clusters of orthologous genes (cogs) shared among ≥99% of all strains (i.e., core genome) was abstracted []. pneumococcal population structure was assessed […]


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Roary institution(s)
Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK; School of Medicine, North Haugh, St Andrews, UK; College of Medicine, Swansea University, Swansea, UK

Roary reviews

 (2)
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Meiski

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Desktop
For those who are used to work in terminal, Roary should not be difficult to use or to install. It has a bunch of software dependencies to run properly and is well documented. Roary can be configured to use specific databases and organisms allowing to change parameters of analysis, enriching your results. Do not require too much computational capability, turning out to be a very powerful tool!!

Korin Albert

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Desktop
I have been Roary to analyze small pangenomes (~20 isolates, ~2.5Mb each) on my laptop. For my small sample set, it runs really fast and works well. Also check the Roary website to see post-analysis programs they recommend; based on the website's suggestion, I visualize Roary output using FriPan.