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Title: GenomePeek—an online tool for prokaryotic genome and metagenome analysis

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:
 [1] ;  [2]
  1. 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
  2. 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:
OSTI Identifier:
1221899
Grant/Contract Number:
AC02-06CH11357
Type:
Accepted Manuscript
Journal Name:
PeerJ
Additional Journal Information:
Journal Volume: 3; Journal ID: ISSN 2167-8359
Publisher:
PeerJ Inc.
Research Org:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Org:
USDOE
Contributing Orgs:
National Science Foundation (NSF), Washington, DC (United States)
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