The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes
By L. Rodriguez-R., Konstantinos T. Konstantinidis. 2016
1,143 citations recorded by the source corpus.
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 underor 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 .
Subfields: Ecology, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/691e1a42017a6515ab046b3e78793dd5cf9e677e
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Ecology
- Ramon Rosselló-Mora
- Konstantinos T. Konstantinidis
- James M. Tiedje
- Jongsik Chun
- James R. Cole
- Sein Park
- Dongwook Kim
- Rob Knight
In Molecular Biology
- Konstantinos T. Konstantinidis
- Ramon Rosselló-Mora
- Jongsik Chun
- James M. Tiedje
- James R. Cole
- William T. Harvey
- Luis Miguel Rodriguez-Rojas
- Santosh Gunturu
Citations in the corpus
- Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity (2021, methodology): “For the AAI calculation, BLAST program (Altschul et al. , 1997) or other packages based on BLAST algorithm, such as the enveomics collection (Rodriguez-R and Konstantinidis, 2016), were used to identify homologous sequences and compute the identity.”
- The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level (2018, background): “rb from the Enveomics collection (11) including a quality report of redundancy and completeness.”