Cargando…

Roary: rapid large-scale prokaryote pan genome analysis

Summary: A typical prokaryote population sequencing study can now consist of hundreds or thousands of isolates. Interrogating these datasets can provide detailed insights into the genetic structure of prokaryotic genomes. We introduce Roary, a tool that rapidly builds large-scale pan genomes, identi...

Descripción completa

Detalles Bibliográficos
Autores principales:	Page, Andrew J., Cummins, Carla A., Hunt, Martin, Wong, Vanessa K., Reuter, Sandra, Holden, Matthew T.G., Fookes, Maria, Falush, Daniel, Keane, Jacqueline A., Parkhill, Julian
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2015
Materias:	Applications Notes
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4817141/ https://www.ncbi.nlm.nih.gov/pubmed/26198102 http://dx.doi.org/10.1093/bioinformatics/btv421

Ejemplares similares

The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries
por: Barquist, Lars, et al.
Publicado: (2016)

Estimating Pangenomes with Roary
por: Sitto, Farrah, et al.
Publicado: (2020)

TAAPP: Tiling Array Analysis Pipeline for Prokaryotes
por: Kumar, Ranjit, et al.
Publicado: (2011)

SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences
por: Coll, Francesc, et al.
Publicado: (2012)

SASpector: analysis of missing genomic regions in draft genomes of prokaryotes
por: Lood, Cédric, et al.
Publicado: (2022)

PanGP: A tool for quickly analyzing bacterial pan-genome profile
por: Zhao, Yongbing, et al.
Publicado: (2014)

Large-scale comparative analysis of microbial pan-genomes using PanOCT
por: Inman, Jason M, et al.
Publicado: (2019)

ProkSeq for complete analysis of RNA-Seq data from prokaryotes
por: Mahmud, A K M Firoj, et al.
Publicado: (2020)

metaSNV v2: detection of SNVs and subspecies in prokaryotic metagenomes
por: Van Rossum, Thea, et al.
Publicado: (2021)

GRiP: a computational tool to simulate transcription factor binding in prokaryotes
por: Zabet, Nicolae Radu, et al.
Publicado: (2012)

DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication
por: Tanizawa, Yasuhiro, et al.
Publicado: (2018)

SpacePHARER: sensitive identification of phages from CRISPR spacers in prokaryotic hosts
por: Zhang, Ruoshi, et al.
Publicado: (2021)

PHIST: fast and accurate prediction of prokaryotic hosts from metagenomic viral sequences
por: Zielezinski, Andrzej, et al.
Publicado: (2021)

PanExplorer: a web-based tool for exploratory analysis and visualization of bacterial pan-genomes
por: Dereeper, Alexis, et al.
Publicado: (2022)

WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs
por: Galiez, Clovis, et al.
Publicado: (2017)

PGAP: pan-genomes analysis pipeline
por: Zhao, Yongbing, et al.
Publicado: (2012)

MSMSpdbb: providing protein databases of closely related organisms to improve proteomic characterization of prokaryotic microbes
por: de Souza, Gustavo A., et al.
Publicado: (2010)

CVTree3 Web Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy
por: Zuo, Guanghong, et al.
Publicado: (2015)

JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison
por: Richter, Michael, et al.
Publicado: (2016)

BAGET 2.0: an updated web tool for the effortless retrieval of prokaryotic gene context and sequence
por: Hepp, Benjamin, et al.
Publicado: (2021)

PGP: parallel prokaryotic proteogenomics pipeline for MPI clusters, high-throughput batch clusters and multicore workstations
por: Tovchigrechko, Andrey, et al.
Publicado: (2014)

LVTree Viewer: An Interactive Display for the All-Species Living Tree Incorporating Automatic Comparison with Prokaryotic Systematics
por: Zuo, Guanghong, et al.
Publicado: (2016)

DNAPlotter: circular and linear interactive genome visualization
por: Carver, Tim, et al.
Publicado: (2009)

IVA: accurate de novo assembly of RNA virus genomes
por: Hunt, Martin, et al.
Publicado: (2015)

BamView: viewing mapped read alignment data in the context of the reference sequence
por: Carver, Tim, et al.
Publicado: (2010)

PanViz: interactive visualization of the structure of functionally annotated pangenomes
por: Pedersen, Thomas Lin, et al.
Publicado: (2017)

PanTools v3: functional annotation, classification and phylogenomics
por: Jonkheer, Eef M, et al.
Publicado: (2022)

ReadItAndKeep: rapid decontamination of SARS-CoV-2 sequencing reads
por: Hunt, Martin, et al.
Publicado: (2022)

PanKmer: k-mer-based and reference-free pangenome analysis
por: Aylward, Anthony J, et al.
Publicado: (2023)

Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data
por: Page, Andrew J., et al.
Publicado: (2016)

PanCGHweb: a web tool for genotype calling in pangenome CGH data
por: Bayjanov, Jumamurat R., et al.
Publicado: (2010)

Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA
por: Holt, Kathryn E., et al.
Publicado: (2009)

Tcbf: a novel user-friendly tool for pan-3D genome analysis of topologically associating domain in eukaryotic organisms
por: He, Xin, et al.
Publicado: (2023)

The CroCo cross-link converter: a user-centred tool to convert results from cross-linking mass spectrometry experiments
por: Bender, Julian, et al.
Publicado: (2020)

Rapid membrane protein topology prediction
por: Hennerdal, Aron, et al.
Publicado: (2011)

PALMsiever: a tool to turn raw data into results for single-molecule localization microscopy
por: Pengo, Thomas, et al.
Publicado: (2015)

WIST: toolkit for rapid, customized LIMS development
por: Huang, Y. Wayne, et al.
Publicado: (2011)

Epock: rapid analysis of protein pocket dynamics
por: Laurent, Benoist, et al.
Publicado: (2015)

RICOPILI: Rapid Imputation for COnsortias PIpeLIne
por: Lam, Max, et al.
Publicado: (2019)

ABACAS: algorithm-based automatic contiguation of assembled sequences
por: Assefa, Samuel, et al.
Publicado: (2009)

Cannot write session to /tmp/vufind_sessions/sess_43njloqh6c841dfo7ugv5jpk8m