KvarQ: targeted and direct variant calling from fastq reads of bacterial genomes. (Q34340287)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25297886 AND SRC:MED&resulttype=core&format=json

20 February 2020

title

KvarQ: targeted and direct variant calling from fastq reads of bacterial genomes (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25297886 AND SRC:MED&resulttype=core&format=json

20 February 2020

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25297886 AND SRC:MED&resulttype=core&format=json

20 February 2020

Mireia Coscolla

3

1 reference

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20 February 2020

Sébastien Gagneux

5

1 reference

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20 February 2020

author name string

Andreas Steiner

1

1 reference

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20 February 2020

Sonia Borrell

4

1 reference

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20 February 2020

language of work or name

English

0 references

publication date

9 October 2014

1 reference

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20 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25297886 AND SRC:MED&resulttype=core&format=json

20 February 2020

volume

15

1 reference

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20 February 2020

page(s)

881

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25297886 AND SRC:MED&resulttype=core&format=json

Predicting extensively drug-resistant Mycobacterium tuberculosis phenotypes with genetic mutations

20 February 2020

cites work

1 reference

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Prevalence and characterization of human mecC methicillin-resistant Staphylococcus aureus isolates in England

6 July 2018

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Genomic comparative analysis and gene function prediction in infectious diseases: application to the investigation of a meningitis outbreak

6 July 2018

1 reference

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Epidemiological investigation of Pseudomonas aeruginosa isolates from a six-year-long hospital outbreak using high-throughput whole genome sequencing

6 July 2018

1 reference

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Bridging genomics technology and biology

6 July 2018

1 reference

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Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts

6 July 2018

1 reference

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Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans

6 July 2018

1 reference

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Rapid diagnostics of tuberculosis and drug resistance in the industrialized world: clinical and public health benefits and barriers to implementation

6 July 2018

1 reference

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Whole-genome sequencing of gentamicin-resistant Campylobacter coli isolated from U.S. retail meats reveals novel plasmid-mediated aminoglycoside resistance genes

6 July 2018

1 reference

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Whole-genome sequencing for rapid susceptibility testing of M. tuberculosis

6 July 2018

1 reference

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Selected insights from application of whole-genome sequencing for outbreak investigations

6 July 2018

1 reference

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Novel Mycobacterium tuberculosis complex isolate from a wild chimpanzee

6 July 2018

1 reference

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Genomics and outbreak investigation: from sequence to consequence

6 July 2018

1 reference

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Rapid bacterial genome sequencing: methods and applications in clinical microbiology

6 July 2018

1 reference

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Public health genomics and the new molecular epidemiology of bacterial pathogens

6 July 2018

1 reference

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Inferring patient to patient transmission of Mycobacterium tuberculosis from whole genome sequencing data

6 July 2018

1 reference

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Contact investigations for outbreaks of Mycobacterium tuberculosis: advances through whole genome sequencing

6 July 2018

1 reference

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Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study

6 July 2018

1 reference

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Bacterial genomes in epidemiology--present and future.

6 July 2018

1 reference

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Phylogeographic variation in recombination rates within a global clone of methicillin-resistant Staphylococcus aureus

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4197298

Single nucleotide polymorphisms in Mycobacterium tuberculosis and the need for a curated database

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4197298

Microevolutionary analysis of Clostridium difficile genomes to investigate transmission

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4197298

Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4197298

Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4197298

Investigation of disease outbreaks with genome sequencing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4197298

Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4197298

Two new rapid SNP-typing methods for classifying mycobacterium tuberculosis complex into the main phylogenetic lineages

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4197298

High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity.

6 July 2018

1 reference

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Short read sequence typing (SRST): multi-locus sequence types from short reads

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4197298

Rapid whole-genome sequencing of bacterial pathogens in the clinical microbiology laboratory--pipe dream or reality?

6 July 2018

1 reference

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Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak

6 July 2018

1 reference

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Bacterial genomics in infectious disease and the clinical pathology laboratory.

6 July 2018

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Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes.

6 July 2018

1 reference

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Bacterial epidemiology and biology - lessons from genome sequencing

6 July 2018

1 reference

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Whole-genome sequencing and social-network analysis of a tuberculosis outbreak

6 July 2018

1 reference

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BIGSdb: Scalable analysis of bacterial genome variation at the population level.

6 July 2018

1 reference

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Does M. tuberculosis genomic diversity explain disease diversity?

6 July 2018

1 reference

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High-throughput sequencing and clinical microbiology: progress, opportunities and challenges

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4197298

Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4197298

Genotyping of genetically monomorphic bacteria: DNA sequencing in Mycobacterium tuberculosis highlights the limitations of current methodologies.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4197298

Fast and accurate short read alignment with Burrows-Wheeler transform

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4197298

Tuberculosis drug resistance mutation database

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4197298

High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4197298

Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4197298

Artemis: sequence visualization and annotation

6 July 2018

1 reference

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Molecular determinants of drug resistance in tuberculosis.

6 July 2018

1 reference

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Molecular genetic basis of antimicrobial agent resistance in Mycobacterium tuberculosis: 1998 update

6 July 2018

1 reference

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Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4197298

Cloning and nucleotide sequence of Mycobacterium tuberculosis gyrA and gyrB genes and detection of quinolone resistance mutations

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4197298

Complex genetics of drug resistance in Mycobacterium tuberculosis.

6 July 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186/1471-2164-15-881

TubercuList--10 years after

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186/1471-2164-15-881

21 January 2018

Identifiers

DOI

10.1186/1471-2164-15-881

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25297886 AND SRC:MED&resulttype=core&format=json

20 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25297886 AND SRC:MED&resulttype=core&format=json

20 February 2020

PubMed publication ID

25297886

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25297886 AND SRC:MED&resulttype=core&format=json