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PeerJ. 2015 Jun 16;3:e1025. doi: 10.7717/peerj.1025. eCollection 2015.

GenomePeek-an online tool for prokaryotic genome and metagenome analysis.

Author information

1
Department of Computer Science, San Diego State University , San Diego, CA , USA ; Department of Biology, San Diego State University , San Diego, CA , USA.
2
Department of Computer Science, San Diego State University , San Diego, CA , USA ; Department of Biology, San Diego State University , San Diego, CA , USA ; Computational Sciences Research Center, San Diego State University , San Diego, CA , USA ; Mathematics and Computer Science Division, Argonne National Laboratory , Argonne, IL , USA.

Abstract

As more and more prokaryotic sequencing takes 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.

KEYWORDS:

Abundance; Archaea; Bacteria; Distribution; Genome; Metagenome; Population; Sequencing; Taxonomic

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