Sequence-based Ultra-Rapid Pathogen Identification

SURPI™ is a computational pipeline for pathogen identification from complex metagenomic next-generation sequencing (NGS) data generated from clinical samples.

Unbiased 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 has been hindered by the bioinformatics challenge of analyzing results accurately and in a clinically relevant timeframe.

Our manuscript describing SURPI™ has been published in Genome Research.

SURPI™ can be installed on a local Ubuntu server or an Amazon EC2 cloud-computing instance. Please note that the SURPI™ pipeline has many open-source software dependencies. Below, we supply links to the source code and outside software requirements as well as an Amazon AMI to automatically set up an EC2 instance using your Amazon AWS account.


SURPI™ is available under the 2-clause BSD license on github.

A script to install SURPI™ locally is available. The script is designed to install SURPI™ and all software dependencies onto a machine running Ubuntu 12.04. The SURPI™ installer can be downloaded here.


We've set up a mailing list at:!forum/surpi to ask questions and/or report bugs.


Which is the correct sequence quality for my data?

SURPI™ supports 2 different methods for coding sequence qualities within a FASTQ file (Sanger & Illumina).

Counterintuitively, the Sanger quality format is likely the method your data is encoded in if you are generating data on an Illumina machine after early 2011. See here, here and here for more information.

Selecting Illumina quality on Sanger data will likely lead to improper preprocessing, resulting in files of 0 length (sample.preprocessing.fastq and sample.cutadapt.fastq)

As of SURPI™ 1.0.17, the pipeline will cease after preprocessing if the resulting files are of 0 length.

SURPI™ is a trademark of The Regents of the University of California.

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