ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads

ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads

Antimicrobial resistance (AMR) is one of the major threats to human and animal health worldwide, yet few high-throughput tools exist to analyse and predict the resistance of a bacterial isolate from sequencing data. Here we present a new tool, ARIBA, that identifies AMR-associated genes and single n...

Descrizione completa

Dettagli Bibliografici
Autori principali:	Hunt, M, Mather, AE, Sánchez-Busó, L, Page, AJ, Parkhill, J, Keane, JA, Harris, SR
Natura:	Journal article
Lingua:	English
Pubblicazione:	Microbiology Society 2017

Documenti analoghi

Rapid multi-locus sequence typing direct from uncorrected long reads using Krocus
di: Andrew J. Page, et al.
Pubblicazione: (2018-07-01)

Using genomics to understand antimicrobial resistance and transmission in Neisseria gonorrhoeae
di: Sanchez-Buso, L, et al.
Pubblicazione: (2019)

ReadItAndKeep: rapid decontamination of SARS-CoV-2 sequencing reads
di: Hunt, M, et al.
Pubblicazione: (2022)

ReadItAndKeep: rapid decontamination of SARS-CoV-2 sequencing reads
di: Hunt, M, et al.
Pubblicazione: (2022)

Identification of highly variable sequence fragments in unmapped reads for rapid bacterial genotyping
di: Marketa Nykrynova, et al.
Pubblicazione: (2022-12-01)

Retours sur le colloque de printemps de l'association francophone des professionnels de la Basse-Vision (ARIBa) de mai 2015 à Paris
di: Emeline Marie Kientz
Pubblicazione: (2015-10-01)

Rapid genotyping of targeted viral samples using Illumina short-read sequencing data.
di: Alex Váradi, et al.
Pubblicazione: (2022-01-01)

Genetic variation regulates the activation and specificity of restriction-modification systems in Neisseria gonorrhoeae
di: Sánchez-Busó, L, et al.
Pubblicazione: (2019)

Contributions of Long-Read Sequencing for the Detection of Antimicrobial Resistance
di: Roberto Sierra, et al.
Pubblicazione: (2024-08-01)

Integrative genotyping of cancer and immune phenotypes by long-read sequencing
di: Livius Penter, et al.
Pubblicazione: (2024-01-01)

Rapid genotype imputation from sequence with reference panels
di: Davies, RW, et al.
Pubblicazione: (2021)

A global resource for genomic predictions of antimicrobial resistance and surveillance of Salmonella Typhi at pathogenwatch
di: Argimón, S, et al.
Pubblicazione: (2021)

Population-scale genotyping of structural variation in the era of long-read sequencing
di: Cheng Quan, et al.
Pubblicazione: (2022-01-01)

Antimicrobial resistance prediction and phylogenetic analysis of Neisseria gonorrhoeae isolates using the Oxford Nanopore MinION sequencer
di: Golparian, D, et al.
Pubblicazione: (2018)

Rapid genotype imputation from sequence without reference panels
di: Myers, S, et al.
Pubblicazione: (2016)

Rapid genotyping of soybean cultivars using high throughput sequencing.
di: Kranthi Varala, et al.
Pubblicazione: (2011-01-01)

Genetic variation associated with infection and the environment in the accidental pathogen Burkholderia pseudomallei
di: Chewapreecha, C, et al.
Pubblicazione: (2019)

Genetic variation associated with infection and the environment in the accidental pathogen Burkholderia pseudomallei
di: Chewapreecha, C, et al.
Pubblicazione: (2019)

Evaluation of DNA extraction kits for long-read shotgun metagenomics using Oxford Nanopore sequencing for rapid taxonomic and antimicrobial resistance detection
di: Srinithi Purushothaman, et al.
Pubblicazione: (2024-11-01)

Rapid Phenotypic and Genotypic Antimicrobial Susceptibility Testing Approaches for Use in the Clinical Laboratory
di: Siham Hattab, et al.
Pubblicazione: (2024-08-01)

Dynamics and impact of homologous recombination on the evolution of Legionella pneumophila
di: David, S, et al.
Pubblicazione: (2017)

LD-based SNP and genotype calling from next-generation sequencing reads.
di: Menelaou, A
Pubblicazione: (2012)

Molecular epidemiology and whole genome sequencing analysis of clinical mycobacterium bovis from Ghana
di: Otchere, ID, et al.
Pubblicazione: (2019)

Evaluation of parameters affecting performance and reliability of machine learning-based antibiotic susceptibility testing from whole genome sequencing data
di: Hicks, AL, et al.
Pubblicazione: (2019)

SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data
di: Epping, L, et al.
Pubblicazione: (2018)

Genotype calling and phasing using next-generation sequencing reads and a haplotype scaffold.
di: Menelaou, A, et al.
Pubblicazione: (2013)

Comprehensive evaluation of structural variant genotyping methods based on long-read sequencing data
di: Xiaoke Duan, et al.
Pubblicazione: (2022-04-01)

Detecting Large Chromosomal Modifications Using Short Read Data From Genotyping-by-Sequencing
di: Jens Keilwagen, et al.
Pubblicazione: (2019-09-01)

Linkage disequilibrium based genotype calling from low-coverage shotgun sequencing reads
di: Wu Yufeng, et al.
Pubblicazione: (2011-02-01)

Paragraph: a graph-based structural variant genotyper for short-read sequence data
di: Sai Chen, et al.
Pubblicazione: (2019-12-01)

Rapid and simple analysis of short and long sequencing reads using DuesselporeTM
di: Christian Vogeley, et al.
Pubblicazione: (2022-08-01)

RapidRat: Development, validation and application of a genotyping-by-sequencing panel for rapid biosecurity and invasive species management.
di: Bryson M F Sjodin, et al.
Pubblicazione: (2020-01-01)

Long‐read genotyping with SLANG (Simple Long‐read loci Assembly of Nanopore data for Genotyping)
di: Marco Dorfner, et al.
Pubblicazione: (2022-05-01)

Straglr: discovering and genotyping tandem repeat expansions using whole genome long-read sequences
di: Readman Chiu, et al.
Pubblicazione: (2021-08-01)

GINDEL: accurate genotype calling of insertions and deletions from low coverage population sequence reads.
di: Chong Chu, et al.
Pubblicazione: (2014-01-01)

Target-enriched long-read sequencing (TELSeq) contextualizes antimicrobial resistance genes in metagenomes
di: Ilya B. Slizovskiy, et al.
Pubblicazione: (2022-11-01)

Genotyping by Sequencing in Almond: SNP Discovery, Linkage Mapping, and Marker Design
di: Shashi N. Goonetilleke, et al.
Pubblicazione: (2018-01-01)

Rapid detection of myeloid neoplasm fusions using single-molecule long-read sequencing.
di: Olga Sala-Torra, et al.
Pubblicazione: (2023-01-01)

Long read sequencing reveals poxvirus evolution through rapid homogenization of gene arrays
di: Thomas A Sasani, et al.
Pubblicazione: (2018-08-01)

Bazam: a rapid method for read extraction and realignment of high-throughput sequencing data
di: Simon P. Sadedin, et al.
Pubblicazione: (2019-04-01)