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Roary: Rapid large-scale prokaryote pan genome analysis [article]

Andrew J Page, Carla A Cummins, Martin Hunt, Vanessa K Wong, Sandra Reuter, Matthew T. G. Holden, Maria Fookes, Jacqueline A Keane, Julian Parkhill
2015 bioRxiv   pre-print
We introduce Roary, a tool that rapidly builds large-scale pan genomes, identifying the core and dispensable accessory genes.  ...  Roary makes construction of the pan genome of thousands of prokaryote samples possible on a standard desktop without compromising on the accuracy of results.  ...  Roary: Rapid large-scale prokaryote pan genome analysis  ... 
doi:10.1101/019315 fatcat:3o5uzr3rovdrxh7wxs5kswwmvu

Roary: rapid large-scale prokaryote pan genome analysis

Andrew J. Page, Carla A. Cummins, Martin Hunt, Vanessa K. Wong, Sandra Reuter, Matthew T.G. Holden, Maria Fookes, Daniel Falush, Jacqueline A. Keane, Julian Parkhill
2015 Bioinformatics  
We introduce Roary, a tool that rapidly builds large-scale pan genomes, identifying the core and accessory genes.  ...  Roary makes construction of the pan genome of thousands of prokaryote samples possible on a standard desktop without compromising on the accuracy of results.  ...  Roary scales well on large real datasets, identifying large numbers of core genes, even in the presence of a varied open pan genome.  ... 
doi:10.1093/bioinformatics/btv421 pmid:26198102 pmcid:PMC4817141 fatcat:olwblb3azfhatbj7x2ets47keu

panX: pan-genome analysis and exploration

Wei Ding, Franz Baumdicker, Richard A Neher
2017 Nucleic Acids Research  
We have developed a pipeline that efficiently identifies orthologous gene clusters in the pan-genome.  ...  Custom pan-genomes can be visualized either using a webserver or by serving panX locally as a browser-based application.  ...  This "divideand-conquer" strategy can be applied repeatedly for very large pan-genomes and keeps scaling of clustering approximately linear, see Fig. 1 .  ... 
doi:10.1093/nar/gkx977 pmid:29077859 pmcid:PMC5758898 fatcat:t7x3n35plvbspclopmh6jdujj4

panX: pan-genome analysis and exploration [article]

Wei Ding, Franz Baumdicker, Richard A Neher
2016 bioRxiv   pre-print
We have developed a pipeline that efficiently identifies orthologous gene clusters in the pan-genome.  ...  Custom pan-genomes can be visualized either using a webserver or by serving panX locally as a browser-based application.  ...  This "divideand-conquer" strategy can be applied repeatedly for very large pan-genomes and keeps scaling of clustering approximately linear, see Fig. 1 .  ... 
doi:10.1101/072082 fatcat:awkdv2s4qrhqvfzhdghcyrkgou

A Review of Pangenome Tools and Recent Studies [chapter]

G. S. Vernikos
2020 The Pangenome  
With the advance of sequencing technologies, the landscape of genomic analysis has been transformed, by moving from single strain to species (or even higher taxa)-wide genomic resolution, toward the direction  ...  Herein we will review, from practical and technical implementation, existing projects of pangenome analysis, with the aim of providing the reader with a snapshot of useful tools should they need to embark  ...  The pipeline consists of three stand-alone tools, namely Prokka v1.11 (Seemann 2014) for rapid prokaryotic genome annotation, panX (Ding et al. 2018 ) for pangenome analysis, and antiSMASH3.0 (Weber  ... 
doi:10.1007/978-3-030-38281-0_4 fatcat:pqmpmbqt6fbwdd3k2xwr75icpa

PanRV: Pangenome-reverse vaccinology approach for identifications of potential vaccine candidates in microbial pangenome

Kanwal Naz, Anam Naz, Shifa Tariq Ashraf, Muhammad Rizwan, Jamil Ahmad, Jan Baumbach, Amjad Ali
2019 BMC Bioinformatics  
The pipeline is tested by using genomic data from 301 genomes of Staphylococcus aureus and the results are verified by experimentally known antigenic data.  ...  To look for broad-spectrum immunogenic targets and analysis of closelyrelated bacterial species, the assimilation of pangenome concept into reverse vaccinology approach is essential.  ...  Roary [23] (rapid large-scale prokaryote pangenome analysis Pipeline) is integrated in PGM for pangenome estimation.  ... 
doi:10.1186/s12859-019-2713-9 fatcat:x6vuvglfcfbqllvluxdvwfqsu4

Disentangling the impact of environmental and phylogenetic constraints on prokaryotic strain diversity [article]

Oleksandr M. Maistrenko, Daniel R. Mende, Mechthild Luetge, Falk Hildebrand, Thomas SB Schmidt, Simone S. Li, Luis Pedro Coelho, Jaime Huerta-Cepas, Shinichi Sunagawa, Peer Bork
2019 bioRxiv   pre-print
Hence, pan-genomes are increasingly used to characterize the strain diversity of prokaryotic species.  ...  strains, we computed pan-genomes for 155 phylogenetically diverse species using 7000 high-quality genomes.  ...  Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 2015; 31: 3691-3693. 31. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30: 2068-2069. 32.  ... 
doi:10.1101/735696 fatcat:454jtye3nneojd65wccn7dk6fq

PATO: Pangenome Analysis Toolkit [article]

Miguel Diez Fernandez-de-Bobadilla, Alba Talavera-Rodriguez, Lucia Chacon, Fernando Baquero, Teresa M. Coque, Val F Lanza
2021 bioRxiv   pre-print
PATO has been developed in R to integrate with the large set of tools available for genetic, phylogenetic and statistical analysis in this environment.  ...  We present the Pangenome Analysis Toolkit (PATO) designed to simultaneously analyze thousands of genomes using a desktop computer.  ...  Genome Biol., 17, 132. Page,A.J. et al. (2015) Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics, 31, 3691-3.  ... 
doi:10.1101/2021.01.30.428878 fatcat:qgxmzikkpvbsvggcn2oz6ouxci

Interest of bacterial pangenome analyses in clinical microbiology

Hussein Anani, Rita Zgheib, Issam Hasni, Didier Raoult, Pierre-Edouard Fournier
2020 Microbial Pathogenesis  
In addition, the significant cost reduction of bacterial whole genome sequencing as well as the rapid increase in the number of available bacterial genomes have prompted the development of pangenomic software  ...  Thanks to the progress and decreasing costs in genome sequencing technologies, more than 250,000 bacterial genomes are currently available in public databases, covering most, if not all, of the major human-associated  ...  Fig. 1 . 1 Evolution of the annual number of publications with 'Bacteria', 'pangenome', 'pan genome' and 'pan-genome' as keywords in Pubmed (https:// www.ncbi.nlm.nih.gov/pubmed/).  ... 
doi:10.1016/j.micpath.2020.104275 pmid:32562810 fatcat:jevw3ku4uvethibt76hldoo7y4

BPGA- an ultra-fast pan-genome analysis pipeline

Narendrakumar M. Chaudhari, Vinod Kumar Gupta, Chitra Dutta
2016 Scientific Reports  
Recent advances in ultra-high-throughput sequencing technology and metagenomics have led to a paradigm shift in microbial genomics from few genome comparisons to large-scale pan-genome studies at different  ...  Here we present an ultra-fast computational pipeline BPGA (Bacterial Pan Genome Analysis tool) with seven functional modules.  ...  Author Contributions N.M.C. and V.K.G. developed the pipeline, performed analysis and drafted the manuscript. C.D. conceived the project and revised the manuscript.  ... 
doi:10.1038/srep24373 pmid:27071527 pmcid:PMC4829868 fatcat:b36p2xo2cbhrfe72fh7d5ad2pu

Pantoea ananatis Genetic Diversity Analysis Reveals Limited Genomic Diversity as Well as Accessory Genes Correlated with Onion Pathogenicity

Shaun P. Stice, Spencer D. Stumpf, Ron D. Gitaitis, Brian H. Kvitko, Bhabesh Dutta
2018 Frontiers in Microbiology  
The lack of focus on a single host system for this phytopathgenic disease necessitates the pan-genomic analysis performed in this study.  ...  Whole genome sequencing and pan-genomic analysis of a sub-set of 10 strains aided in the identification of a novel series of genetic regions, likely plasmid borne, and correlating with onion pathogenicity  ...  Pan-Genomic Comparative Analysis of P. ananatis Strains from Georgia The ROARY pan genomic analysis identified a core genome consisting of 3,750 protein coding sequences (CDS) and an accessory genome consisting  ... 
doi:10.3389/fmicb.2018.00184 pmid:29491851 pmcid:PMC5817063 fatcat:izzima7jpnel7odfmiuzf7p4ge

Bactopia: a flexible pipeline for complete analysis of bacterial genomes [article]

Robert A. Petit, Timothy D. Read
2020 bioRxiv   pre-print
BaTs include pan-genome analysis, computing average nucleotide identity between samples, extracting and profiling the 16S genes and taxonomic classification using highly conserved genes.  ...  Bactopia is an open source system that can scale from projects as small as one bacterial genome to thousands that allows for great flexibility in choosing comparison datasets and options for downstream  ...  https://github.com/hyattpd/Prodigal (65) Prokka 1.4.5 Rapid prokaryotic genome annotation https://github.com/tseemann/prokka (28) Roary 3.13.0 Rapid large-scale prokaryote pan genome analysis  ... 
doi:10.1101/2020.02.28.969394 fatcat:f37asai4b5cvbehgvwn7ekmq3u

In-Depth Genomic Characterization of a Meropenem-nonsusceptible Pseudomonas otitidis Strain Contaminating Chicken Carcass

Tatiana Regina Vieira, Gustavo Enck Sambrano, Núbia Michelle Vieira da Silva, Priscylla Carvalho Vasconcelos, Esther Ferraza Cavinatto de Oliveira, Celso José Bruno de Oliveira, Samuel Paulo Cibulski, Marisa Cardoso
2020 Acta Scientiae Veterinariae  
Pseudomonas otitidis-pan genome was built using Roary-rapid large-scale prokaryote pan genome analysis using the present strain (K_25) and other two P. otitidis genomes (PAM-1, DSM 17224) publicly available  ...  The core genome analysis of the two human strains resulted in similar percentages.Discussion: Carbapenems are critically important drugs for human health and bacterial strains resistant to these antimicrobials  ...  Roary-rapid large-scale prokaryote pan genome analysis (academic.oup.com/ bioinformatics/article-lookup/doi/10.1093/bioinformatics/btv421) was used to build a pangenome.  ... 
doi:10.22456/1679-9216.103176 fatcat:bxitrnjo75d3nheuzuzfv3uohi

Diagnostic Sequences That Distinguish M. avium Subspecies Strains

John P. Bannantine, Judith R. Stabel, Darrell O. Bayles, Cyril Conde, Franck Biet
2021 Frontiers in Veterinary Science  
We have conducted a comprehensive comparison of these genomes using two independent pan genomic comparison tools, PanOCT and Roary.  ...  The majority of these genes are arranged in clusters called genomic islands.  ...  These analyses included Roary (23) and PanOCT (24) pan genome tools, which identify core and accessory genes for a group of closely related organisms.  ... 
doi:10.3389/fvets.2020.620094 pmid:33585607 pmcid:PMC7876471 fatcat:zdlg3vvlx5ghxcwlvmen2f5vyy

Complete Genome Sequence and Comparative Analysis of Staphylococcus condimenti DSM 11674, a Potential Starter Culture Isolated from Soy Sauce Mash

Huihui Dong, Jian Chen, Andrew K. Hastings, Lihua Guo, Beiwen Zheng
2017 Frontiers in Bioengineering and Biotechnology  
Comparative Genomic analysis The core genome alignment module in the rapid large-scale prokaryote pan genome analysis (Roary) pipeline was used to extract predicted coding regions from 21 complete Staphylococci  ...  the Rapid Annotation using Subsystem Technology server (Aziz et al., 2008) and the NCBI Prokaryotic Genome Annotation Pipeline.  ... 
doi:10.3389/fbioe.2017.00056 pmid:29057223 pmcid:PMC5635325 fatcat:cvxegzgffvc3jhkjf55knj7jt4
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