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


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.





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Publication Info

Naccache, Samia N, Scot Federman, Narayanan Veeraraghavan, Matei Zaharia, Deanna Lee, Erik Samayoa, Jerome Bouquet, Alexander L Greninger, et al. (2014). A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples. Genome Res, 24(7). pp. 1180–1192. 10.1101/gr.171934.113 Retrieved from https://hdl.handle.net/10161/13772.

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John Andrew Crump

Adjunct Professor in the Department of Medicine

I am based in northern Tanzania where I am Site Leader for Duke University’s collaborative research program based at Kilimanjaro Christian Medical Centre and Director of Tanzania Operations for the Duke Global Health Institute. I oversee the design and implementation of research studies on infectious diseases, particularly febrile illness, invasive bacterial disease, HIV-associated opportunistic infections, clinical trials of antiretroviral therapy and prevention of mother-to-child transmission of HIV, and infectious diseases diagnostics. In addition, I am a medical epidemiologist with the US Centers for Disease Control and Prevention (CDC). My CDC work focuses on enteric infection epidemiology and prevention in developing countries, particularly invasive salmonelloses.

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