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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
biochemistry, genetics and molecular biology
A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples
Genome Research, Volume 24, No. 7, Year 2014
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Description
Unbiased next-generation sequencing (NGS) approaches enable comprehensive pathogen detection in the clinical microbiology laboratory and have numerous applications for public health surveillance, outbreak investigation, and the diagnosis of infectious diseases. However, practical deployment of the technology is hindered by the bioinformatics challenge of analyzing results accurately and in a clinically relevant timeframe. Here we describe SURPI ("sequence-based ultrarapid pathogen identification"), a computational pipeline for pathogen identification from complex metagenomic NGS data generated from clinical samples, and demonstrate use of the pipeline in the analysis of 237 clinical samples comprising more than 1.1 billion sequences. Deployable on both cloud-based and standalone servers, SURPI leverages two state-of-the-art aligners for accelerated analyses, SNAP and RAPSearch, which are as accurate as existing bioinformatics tools but orders of magnitude faster in performance. In fast mode, SURPI detects viruses and bacteria by scanning data sets of 7-500 million reads in 11 min to 5 h, while in comprehensive mode, all known microorganisms are identified, followed by de novo assembly and protein homology searches for divergent viruses in 50 min to 16 h. SURPI has also directly contributed to real-time microbial diagnosis in acutely ill patients, underscoring its potential key role in the development of unbiased NGS-based clinical assays in infectious diseases that demand rapid turnaround times. © 2014 Naccache et al.
Authors & Co-Authors
Naccache, Samia N.
United States, San Francisco
University of California, San Francisco
United States, Santa Clara
Abbott Diagnostics
Federman, Scot
United States, San Francisco
University of California, San Francisco
United States, Santa Clara
Abbott Diagnostics
Veeraraghavan, Narayanan
United States, San Francisco
University of California, San Francisco
United States, Santa Clara
Abbott Diagnostics
Zaharia, Matei
United States, Berkeley
University of California, Berkeley
Lee, Deanna C.
United States, San Francisco
University of California, San Francisco
United States, Santa Clara
Abbott Diagnostics
Samayoa, Erik
United States, San Francisco
University of California, San Francisco
United States, Santa Clara
Abbott Diagnostics
Bouquet, Jérôme
United States, San Francisco
University of California, San Francisco
United States, Santa Clara
Abbott Diagnostics
Greninger, Alexander L.
United States, San Francisco
University of California, San Francisco
Luk, Kacheung
United States, Santa Clara
Abbott Diagnostics
Enge, Barryett A.
United States, Berkeley
Viral Rickettsial Disease Laboratory
Wadford, Debra A.
United States, Berkeley
Viral Rickettsial Disease Laboratory
Messenger, Sharon L.
United States, Berkeley
Viral Rickettsial Disease Laboratory
Genrich, Gillian L.
United States, San Francisco
University of California, San Francisco
Pellegrino, Kristen
United States, San Francisco
University of California, San Francisco
Grard, Gilda
Gabon, Franceville
Centre International de Recherches Medicales de Franceville
Leroy, Éric Maurice
Gabon, Franceville
Centre International de Recherches Medicales de Franceville
Schneider, Bradley S.
United States, San Francisco
Metabiota, Inc.
Fair, Joseph N.
United States, San Francisco
Metabiota, Inc.
Martínez, Miguel A.
Mexico, Cuernavaca
Instituto de Biotecnología de la Unam
Isa, Pavel
Mexico, Cuernavaca
Instituto de Biotecnología de la Unam
Crump, John A.
United States, Durham
Duke University Medical Center
Tanzania, Moshi
Kilimanjaro Christian Medical Centre
New Zealand, Dunedin
University of Otago
DeRisi, Joseph L.
United States, San Francisco
University of California, San Francisco
Sittler, Taylor
United States, San Francisco
University of California, San Francisco
Hackett, John R.
United States, Santa Clara
Abbott Diagnostics
Miller, Steve A.
United States, San Francisco
University of California, San Francisco
United States, Santa Clara
Abbott Diagnostics
Chiu, Charles Y.
United States, San Francisco
University of California, San Francisco
United States, Santa Clara
Abbott Diagnostics
Statistics
Citations: 416
Authors: 26
Affiliations: 10
Identifiers
Doi:
10.1101/gr.171934.113
ISSN:
10889051
e-ISSN:
15495469