GenomePeek-an online tool for prokaryotic genome and metagenome analysis

Katelyn McNair; Robert A Edwards

doi:10.7717/peerj.1025

GenomePeek-an online tool for prokaryotic genome and metagenome analysis

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

Authors

Katelyn McNair¹, Robert A Edwards²

Affiliations

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.

Grants and funding

This work was supported by grants from the National Science Foundation [DBI-0850356, MCB-1330800, and DEB-1046413]. High performance computation was provided by award CNS-1305112 from the Information and Intelligent Systems Division of the National Science Foundation. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.