The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes

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1 School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States
2 Center for Bioinformatics and Computational Genomics, Georgia Institute of Technology, Atlanta, Georgia, United States
3 School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States
DOI
10.7287/peerj.preprints.1900v1
Published
Accepted
Subject Areas
Bioinformatics, Genomics, Microbiology
Keywords
Genomics, Metagenomics, Graphical User Interface, Toolkit
Copyright
© 2016 Rodriguez-R 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
Rodriguez-R LM, Konstantinidis KT. 2016. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Preprints 4:e1900v1

Abstract

Genomic and metagenomic analyses are increasingly becoming commonplace in several areas of biological research, but recurrent specialized analyses are frequently reported as in-house scripts rarely available after publication. We describe the enveomics collection, a growing set of actively maintained scripts for several recurrent and specialized tasks in microbial genomics and metagenomics, and present a graphical user interface and several case studies. Our resource includes previously described as well as new algorithms such as Transformed-space Resampling In Biased Sets (TRIBS), a novel method to evaluate phylogenetic under- or over-dispersion in reference sets with strong phylogenetic bias. The enveomics collection is freely available under the terms of the Artistic License 2.0 at https://github.com/lmrodriguezr/enveomics and for online analysis at http://enve-omics.ce.gatech.edu

Author Comment

This is a submission to PeerJ for review.

Supplemental Information

List of scripts and functions currently available in the enveomics collection

For an updated categorized list visit http://enve-omics.ce.gatech.edu/enveomics/docs .

DOI: 10.7287/peerj.preprints.1900v1/supp-1

Conceptual workflow of the TRIBS algorithm applied to phylogenetic distances

The TRIBS (Transformed-space Resampling In Biased Sets) algorithm is described in the main text. The entire set (i.e., phylogenetic space of genomes or genome-derived features) is represented in black and the selected subset for evaluation (i.e., genomes presenting the trait of interest) is represented in burgundy. Median is abbreviated as Med.

DOI: 10.7287/peerj.preprints.1900v1/supp-2