Roary pipeline

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

 (7)
2018
PMCID: 5940178
PMID: 29738521
DOI: 10.1371/journal.pgen.1007333

[…] from the supplementary material of nuccio and bäumler [17]. a core gene phylogeny for the strains used to build the model was produced using raxml [76], based on a core gene alignment created in roary [77]., profile hidden markov models (hmms) for gammaproteobacterial proteins were retrieved from the eggnog database [30]. we chose this source of hmms because it is publicly available, […]

2017
PMCID: 5278652
PMID: 28138345
DOI: 10.7150/jgen.17863

[…] jspecies v1.2.1 10. phylophlan v0.99 was subsequently used to infer the evolutionary relationship among the sequenced strains and related strains/species 11., pangenome analysis was performed with roary (https://sanger-pathogens.github.io/roary/) using a protein identity cut-off of 90% for clustering orthologs. genus delineation was determined based on the percentage of conserved proteins […]

2017
PMCID: 5386241
PMID: 28394899
DOI: 10.1371/journal.pone.0175330

[…] codon readthrough. we used the stand-alone prokka program [17] to re-annotate 20 complete genome sequences (table 1), excluding nitr202 strain due to unexpected nucleotide designations. based on roary results [18], the core genome included 2,623 orthologous genes and the pan-genome included 7,591 genes (fig 3a and 3b), indicating that different annotation processes affected core […]

2017
PMCID: 5597760
PMID: 28912319
DOI: 10.1128/genomeA.00963-17

[…] m. chimaera genomes using mauve 2.3.1 (14). genomic features were identified and annotated using the ncbi prokaryotic genome automatic annotation pipeline. we conducted core genome comparisons with roary (15)., the m. chimaera sj42 genome consists of three scaffolds, equaling 5,937,236 bp (a 5,891,694-bp chromosome, 33,560-bp plasmid, and 13,458-bp plasmid) and a g+c content of 67.52%. […]

2017
PMCID: 5626246
PMID: 28475476
DOI: 10.1080/21505594.2017.1325064

[…] (http://www.ebi.ac.uk/ena/data/view/prjeb17079). reads from the isolates were assembled using spades,57 annotated using prokka,58 and the core and pan-genome of the isolates was estimated using roary.59 the alignment of the core genome from roary was used as input to create a phylogenetic tree using raxml60 with 100 bootstrap supports. the phylogenetic tree and accessory genome heatmap […]

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.