GenomePeek - An online tool for prokaryotic and metagenome analysis
- Published
- Accepted
- Subject Areas
- Bioinformatics, Computational Biology, Genomics, Microbiology
- Keywords
- genome, metagenome, taxonomic, bacteria, sequencing, population, distribution, archaea, abundance
- Copyright
- © 2014 McNair et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.
- Cite this article
- 2014. GenomePeek - An online tool for prokaryotic and metagenome analysis. PeerJ PrePrints 2:e525v1 https://doi.org/10.7287/peerj.preprints.525v1
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.
Author Comment
This is a resubmission to PeerJ.
Supplemental Information
Supplementary Tables
The abundace data and run times of the various sequence files, by the four different analysis tools.