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 =
}