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SURPI specifications


Unique identifier OMICS_04623
Alternative name Sequence-based Ultra-Rapid Pathogen Identification
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


Publication for Sequence-based Ultra-Rapid Pathogen Identification

SURPI citations


Overview of Virus Metagenomic Classification Methods and Their Biological Applications

Front Microbiol
PMCID: 5924777
PMID: 29740407
DOI: 10.3389/fmicb.2018.00749

[…] tavir, MetLab, SMART, Taxonomer and Virana), or hours (19 workflows: Giant Virus Finder, GOTTCHA, IMSA, MEGAN, MePIC, MetaShot, Metavir 2, NBC, ProViDE, Readscan, Rega Typing Tool, RIEMS, RINS, SLIM, SURPI, Taxy-Pro, “Unknown pathogens from mixed clinical samples,” VIP and ViromeScan), or even days (5 workflows: Exhaustive Iterative Assembly, ViralFusionSeq, VirFind, VirusFinder and VirusSeq). […]


Surveillance of Foodborne Pathogens: Towards Diagnostic Metagenomics of Fecal Samples

PMCID: 5793167
PMID: 29300319
DOI: 10.3390/genes9010014

[…] xonomy-dependent methods have been first described by Mande et al. [], while their performance has been tested by Lindgreen et al. []. A dedicated bioinformatics pipeline for diagnostic metagenomics, sequence-based ultra-rapid pathogen identification (SURPI), was published by Naccache et al., in 2017 []. It is a reference-based pipeline that uses, in a comprehensive mode, the national center for b […]


Nanopore DNA Sequencing and Genome Assembly on the International Space Station

Sci Rep
PMCID: 5740133
PMID: 29269933
DOI: 10.1038/s41598-017-18364-0

[…] e SURPIrt pipeline is a real-time analysis pipeline for automated metagenomic pathogen detection and reference-based genomic assembly from nanopore sequencing data. Modeled after previously published SURPI and Metapore software, SURPIrt incorporates Linux shell scripts and code from the Python, Perl, Javascript, HTML, and Go programming languages. SURPIrt is currently being developed for analysis […]


Diagnosis of Fatal Human Case of Saint Louis Encephalitis Virus Infection by Metagenomic Sequencing, California, 2016

PMCID: 5621550
PMID: 28930022
DOI: 10.3201/eid2310.161986

[…] ). RNA and DNA sequencing libraries from CSF yielded 8,056,471 and 9,083,963 sequence reads, respectively. In the RNA library, 236,615 (2.9%) of the reads were identified as SLEV by using the SURPI+ (sequence-based ultra-rapid pathogen identification) computational pipeline (), with recovery of 99.4% of the predicted 10,936-bp virus genome. Subsequent mNGS testing of the patient’s CSF from hospita […]


Metagenomic based Surveillance of Pacific Coast tick Dermacentor occidentalis Identifies Two Novel Bunyaviruses and an Emerging Human Ricksettsial Pathogen

Sci Rep
PMCID: 5612965
PMID: 28947798
DOI: 10.1038/s41598-017-12047-6
call_split See protocol

[…] sed by Bioanalyzer (Agilent). Sequencing was performed over 4 lanes of 100 base pair (bp) paired-end run on a HiSeq. 2500 (Illumina).Metagenomics sequencing datasets were analyzed for pathogens using SURPI, a bioinformatics pipeline for pathogen detection and discovery. We first computationally subtracted tick sequences from the metagenomic data using the nucleotide aligner SNAP. As the D. occiden […]


Identification of diverse viruses in upper respiratory samples in dromedary camels from United Arab Emirates

PLoS One
PMCID: 5597213
PMID: 28902913
DOI: 10.1371/journal.pone.0184718

[…] Data was primarily analyzed using the SURPI pipeline with standard parameters []. Briefly, Illumina reads were trimmed and classified by read mapping to the NCBI nt database. Unclassified reads were de novo assembled, and the resulting co […]


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SURPI institution(s)
Department of Laboratory Medicine, UCSF, San Francisco, CA, USA

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