GenomePeek—an online tool for prokaryotic genome and metagenome analysis
Abstract
As increases in prokaryotic sequencing take place, a method to quickly and accurately analyze this data is needed. Previous tools are mainly designed for metagenomic analysis and have limitations; such as long runtimes and significant false positive error rates. The online tool GenomePeek (edwards.sdsu.edu/GenomePeek) was developed to analyze both single genome and metagenome sequencing files, quickly and with low error rates. GenomePeek uses a sequence assembly approach where reads to a set of conserved genes are extracted, assembled and then aligned against the highly specific reference database. GenomePeek was found to be faster than traditional approaches while still keeping error rates low, as well as offering unique data visualization options.
- Authors:
-
- San Diego State University, San Diego, CA (United States). Department of Computer Science; San Diego State University, San Diego, CA (United States). Department of Biology
- San Diego State University, San Diego, CA (United States). Department of Computer Science; San Diego State University, San Diego, CA (United States). Department of Biology; San Diego State University, San Diego, CA (United States). Computational Sciences Research Center; Argonne National Lab. (ANL), Argonne, IL (United States)
- Publication Date:
- Research Org.:
- Argonne National Laboratory (ANL), Argonne, IL (United States)
- Sponsoring Org.:
- USDOE
- Contributing Org.:
- National Science Foundation (NSF), Washington, DC (United States)
- OSTI Identifier:
- 1221899
- Grant/Contract Number:
- AC02-06CH11357
- Resource Type:
- Accepted Manuscript
- Journal Name:
- PeerJ
- Additional Journal Information:
- Journal Volume: 3; Journal ID: ISSN 2167-8359
- Publisher:
- PeerJ Inc.
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 97 MATHEMATICS AND COMPUTING; Genome; Metagenome; Taxonomic; Bacteria; Sequencing; Population; Distribution; Archaea; Abundance
Citation Formats
McNair, Katelyn, and Edwards, Robert A. GenomePeek—an online tool for prokaryotic genome and metagenome analysis. United States: N. p., 2015.
Web. doi:10.7717/peerj.1025.
McNair, Katelyn, & Edwards, Robert A. GenomePeek—an online tool for prokaryotic genome and metagenome analysis. United States. https://doi.org/10.7717/peerj.1025
McNair, Katelyn, and Edwards, Robert A. Tue .
"GenomePeek—an online tool for prokaryotic genome and metagenome analysis". United States. https://doi.org/10.7717/peerj.1025. https://www.osti.gov/servlets/purl/1221899.
@article{osti_1221899,
title = {GenomePeek—an online tool for prokaryotic genome and metagenome analysis},
author = {McNair, Katelyn and Edwards, Robert A.},
abstractNote = {As increases in prokaryotic sequencing take place, a method to quickly and accurately analyze this data is needed. Previous tools are mainly designed for metagenomic analysis and have limitations; such as long runtimes and significant false positive error rates. The online tool GenomePeek (edwards.sdsu.edu/GenomePeek) was developed to analyze both single genome and metagenome sequencing files, quickly and with low error rates. GenomePeek uses a sequence assembly approach where reads to a set of conserved genes are extracted, assembled and then aligned against the highly specific reference database. GenomePeek was found to be faster than traditional approaches while still keeping error rates low, as well as offering unique data visualization options.},
doi = {10.7717/peerj.1025},
journal = {PeerJ},
number = ,
volume = 3,
place = {United States},
year = {Tue Jun 16 00:00:00 EDT 2015},
month = {Tue Jun 16 00:00:00 EDT 2015}
}
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