RT Journal
A1 Naccache, Samia N.
A1 Federman, Scot
A1 Veeraraghavan, Narayanan
A1 Zaharia, Matei
A1 Lee, Deanna
A1 Samayoa, Erik
A1 Bouquet, Jerome
A1 Greninger, Alexander L.
A1 Luk, Ka-Cheung
A1 Enge, Barryett
A1 Wadford, Debra A.
A1 Messenger, Sharon L.
A1 Genrich, Gillian L.
A1 Pellegrino, Kristen
A1 Grard, Gilda
A1 Leroy, Eric
A1 Schneider, Bradley S.
A1 Fair, Joseph N.
A1 Martínez, Miguel A.
A1 Isa, Pavel
A1 Crump, John A.
A1 DeRisi, Joseph L.
A1 Sittler, Taylor
A1 Hackett, John
A1 Miller, Steve
A1 Chiu, Charles Y.
T1 A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples
JF Genome Research 
JO Genome Research 
YR 2014 
FD July 01 
VO 24 
IS 7 
SP 1180 
OP 1192 
DO 10.1101/gr.171934.113 
UL http://genome.cshlp.org/content/24/7/1180.abstract 
AB 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.