A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples (Q33839439)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24899342%20AND%20SRC:MED&resulttype=core&format=json

20 March 2020

title

A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples (English)

1 reference

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20 March 2020

1 reference

26

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20 March 2020

Jerome Bouquet

7

1 reference

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20 March 2020

Alexander L. Greninger

8

1 reference

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20 March 2020

Eric M Leroy

16

1 reference

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20 March 2020

Bradley S Schneider

17

1 reference

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20 March 2020

15

Gilda Grard

1 reference

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20 March 2020

11

Debra A Wadford

1 reference

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20 March 2020

18

Joseph N Fair

1 reference

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20 March 2020

author name string

Samia N Naccache

1

1 reference

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20 March 2020

Scot Federman

2

1 reference

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20 March 2020

Narayanan Veeraraghavan

3

1 reference

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20 March 2020

Matei Zaharia

4

1 reference

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20 March 2020

Deanna Lee

5

1 reference

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20 March 2020

Erik Samayoa

6

1 reference

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20 March 2020

Ka-Cheung Luk

9

1 reference

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20 March 2020

Barryett Enge

10

1 reference

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20 March 2020

Sharon L Messenger

12

1 reference

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20 March 2020

Gillian L Genrich

13

1 reference

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20 March 2020

Kristen Pellegrino

14

1 reference

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20 March 2020

Miguel A Martínez

19

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20 March 2020

Pavel Isa

20

1 reference

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20 March 2020

John A Crump

21

1 reference

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20 March 2020

Joseph L DeRisi

22

1 reference

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20 March 2020

Taylor Sittler

23

1 reference

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20 March 2020

John Hackett

24

1 reference

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20 March 2020

Steve Miller

25

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20 March 2020

publication date

4 June 2014

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20 March 2020

1 reference

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20 March 2020

volume

24

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20 March 2020

issue

7

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20 March 2020

page(s)

1180-1192

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Actionable diagnosis of neuroleptospirosis by next-generation sequencing

20 March 2020

cites work

1 reference

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Hantavirus infections among overnight visitors to Yosemite National Park, California, USA, 2012

5 July 2018

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First FDA authorization for next-generation sequencer

5 July 2018

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Identification of novel viruses using VirusHunter--an automated data analysis pipeline

5 July 2018

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GenomeTools: a comprehensive software library for efficient processing of structured genome annotations

5 July 2018

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The genomics of emerging pathogens

5 July 2018

1 reference

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Etiology of severe non-malaria febrile illness in Northern Tanzania: a prospective cohort study

5 July 2018

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5 July 2018

Viral pathogen discovery

1 reference

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IMSA: integrated metagenomic sequence analysis for identification of exogenous reads in a host genomic background

5 July 2018

1 reference

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VirusFinder: software for efficient and accurate detection of viruses and their integration sites in host genomes through next generation sequencing data

5 July 2018

1 reference

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Arboviral diseases and malaria in Australia, 2010-11: annual report of the National Arbovirus and Malaria Advisory Committee

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

The genome sequence of Lone Star virus, a highly divergent bunyavirus found in the Amblyomma americanum tick

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

Prediction and prevention of the next pandemic zoonosis

5 July 2018

1 reference

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READSCAN: a fast and scalable pathogen discovery program with accurate genome relative abundance estimation

5 July 2018

1 reference

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Discovery of a novel polyomavirus in acute diarrheal samples from children

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

Assuring the quality of next-generation sequencing in clinical laboratory practice

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

A novel rhabdovirus associated with acute hemorrhagic fever in central Africa

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

CaPSID: a bioinformatics platform for computational pathogen sequence identification in human genomes and transcriptomes.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

Sequence analysis of the human virome in febrile and afebrile children

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

Diarrhea etiology in a pediatric emergency department: a case control study

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

Next-generation and whole-genome sequencing in the diagnostic clinical microbiology laboratory

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

Fast gapped-read alignment with Bowtie 2

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

Rapid identification of non-human sequences in high-throughput sequencing datasets.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

A distinct lineage of influenza A virus from bats

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

Metagenomic analysis of fever, thrombocytopenia and leukopenia syndrome (FTLS) in Henan Province, China: discovery of a new bunyavirus

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

Genomic analysis identifies association of Fusobacterium with colorectal carcinoma

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

Cross-species transmission of a novel adenovirus associated with a fulminant pneumonia outbreak in a new world monkey colony

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

PathSeq: software to identify or discover microbes by deep sequencing of human tissue

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

Next generation sequence assembly with AMOS.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

Quality control and preprocessing of metagenomic datasets

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

A metagenomic analysis of pandemic influenza A (2009 H1N1) infection in patients from North America

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

Genetic detection and characterization of Lujo virus, a new hemorrhagic fever-associated arenavirus from southern Africa

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

Fast and accurate short read alignment with Burrows-Wheeler transform

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

ABySS: a parallel assembler for short read sequence data

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

Predictors of 30-day mortality and hospital costs in patients with ventilator-associated pneumonia attributed to potentially antibiotic-resistant gram-negative bacteria

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

Diagnostic approaches for patients with suspected encephalitis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

Understanding diagnostic tests 3: Receiver operating characteristic curves

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

Minimus: a fast, lightweight genome assembler

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

Genome sequence of the human malaria parasite Plasmodium falciparum

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

Etiology of acute gastroenteritis in hospitalized children in Melbourne, Australia, from April 1980 to March 1993.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

Receiver-operating characteristic (ROC) plots: a fundamental evaluation tool in clinical medicine.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

Basic local alignment search tool

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

Adding pathogens by genomic subtraction.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

Characterization of viral agents causing acute respiratory infection in a San Francisco University Medical Center Clinic during the influenza season

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

A case-control study of acute respiratory tract infection in general practice patients in The Netherlands

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

Neuroinvasion during delayed primary HHV-7 infection in an immunocompetent adult with encephalitis and flaccid paralysis

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4079973

29 October 2018

Identifiers

DOI

10.1101/GR.171934.113

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24899342%20AND%20SRC:MED&resulttype=core&format=json

20 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24899342%20AND%20SRC:MED&resulttype=core&format=json

20 March 2020

PubMed publication ID

24899342

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24899342%20AND%20SRC:MED&resulttype=core&format=json