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Title: Rapid Threat Organism Recognition Pipeline

Abstract

The RAPTOR computational pipeline identifies microbial nucleic acid sequences present in sequence data from clinical samples. It takes as input raw short-read genomic sequence data (in particular, the type generated by the Illumina sequencing platforms) and outputs taxonomic evaluation of detected microbes in various human-readable formats. This software was designed to assist in the diagnosis or characterization of infectious disease, by detecting pathogen sequences in nucleic acid sequence data from clinical samples. It has also been applied in the detection of algal pathogens, when algal biofuel ponds became unproductive. RAPTOR first trims and filters genomic sequence reads based on quality and related considerations, then performs a quick alignment to the human (or other host) genome to filter out host sequences, then performs a deeper search against microbial genomes. Alignment to a protein sequence database is optional. Alignment results are summarized and placed in a taxonomic framework using the Lowest Common Ancestor algorithm.

Authors:
; ;
Publication Date:
Research Org.:
Sandia National Laboratories (SNL), Albuquerque, NM, and Livermore, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1231698
Report Number(s):
RAPTOR V.2.0; 002926WKSTN00
DOE Contract Number:  
AC04-94AL85000
Resource Type:
Software
Software Revision:
00
Software Package Number:
002926
Software Package Contents:
Open Source Software package available from Sandia National Laboratory at the following URL: http://bioinformatics.sandia.gov/software/
Software CPU:
WKSTN
Open Source:
Yes
Source Code Available:
Yes
Country of Publication:
United States

Citation Formats

Williams, Kelly P., Solberg, Owen D., and Schoeniger, Joseph S. Rapid Threat Organism Recognition Pipeline. Computer software. https://www.osti.gov//servlets/purl/1231698. Vers. 00. USDOE. 7 May. 2013. Web.
Williams, Kelly P., Solberg, Owen D., & Schoeniger, Joseph S. (2013, May 7). Rapid Threat Organism Recognition Pipeline (Version 00) [Computer software]. https://www.osti.gov//servlets/purl/1231698.
Williams, Kelly P., Solberg, Owen D., and Schoeniger, Joseph S. Rapid Threat Organism Recognition Pipeline. Computer software. Version 00. May 7, 2013. https://www.osti.gov//servlets/purl/1231698.
@misc{osti_1231698,
title = {Rapid Threat Organism Recognition Pipeline, Version 00},
author = {Williams, Kelly P. and Solberg, Owen D. and Schoeniger, Joseph S.},
abstractNote = {The RAPTOR computational pipeline identifies microbial nucleic acid sequences present in sequence data from clinical samples. It takes as input raw short-read genomic sequence data (in particular, the type generated by the Illumina sequencing platforms) and outputs taxonomic evaluation of detected microbes in various human-readable formats. This software was designed to assist in the diagnosis or characterization of infectious disease, by detecting pathogen sequences in nucleic acid sequence data from clinical samples. It has also been applied in the detection of algal pathogens, when algal biofuel ponds became unproductive. RAPTOR first trims and filters genomic sequence reads based on quality and related considerations, then performs a quick alignment to the human (or other host) genome to filter out host sequences, then performs a deeper search against microbial genomes. Alignment to a protein sequence database is optional. Alignment results are summarized and placed in a taxonomic framework using the Lowest Common Ancestor algorithm.},
url = {https://www.osti.gov//servlets/purl/1231698},
doi = {},
url = {https://www.osti.gov/biblio/1231698}, year = {Tue May 07 00:00:00 EDT 2013},
month = {Tue May 07 00:00:00 EDT 2013},
note =
}