Luis M Rodriguez-R1, Konstantinos T Konstantinidis. 1. Center for Bioinformatics and Computational Genomics, School of Biology and School of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Drive, Ford ES&T Building, Suite 3224, Atlanta, GA 30332, USA.
Abstract
MOTIVATION: Determining the fraction of the diversity within a microbial community sampled and the amount of sequencing required to cover the total diversity represent challenging issues for metagenomics studies. Owing to these limitations, central ecological questions with respect to the global distribution of microbes and the functional diversity of their communities cannot be robustly assessed. RESULTS: We introduce Nonpareil, a method to estimate and project coverage in metagenomes. Nonpareil does not rely on high-quality assemblies, operational taxonomic unit calling or comprehensive reference databases; thus, it is broadly applicable to metagenomic studies. Application of Nonpareil on available metagenomic datasets provided estimates on the relative complexity of soil, freshwater and human microbiome communities, and suggested that ∼200 Gb of sequencing data are required for 95% abundance-weighted average coverage of the soil communities analyzed. AVAILABILITY AND IMPLEMENTATION: Nonpareil is available at https://github.com/lmrodriguezr/nonpareil/ under the Artistic License 2.0.
MOTIVATION: Determining the fraction of the diversity within a microbial community sampled and the amount of sequencing required to cover the total diversity represent challenging issues for metagenomics studies. Owing to these limitations, central ecological questions with respect to the global distribution of microbes and the functional diversity of their communities cannot be robustly assessed. RESULTS: We introduce Nonpareil, a method to estimate and project coverage in metagenomes. Nonpareil does not rely on high-quality assemblies, operational taxonomic unit calling or comprehensive reference databases; thus, it is broadly applicable to metagenomic studies. Application of Nonpareil on available metagenomic datasets provided estimates on the relative complexity of soil, freshwater and human microbiome communities, and suggested that ∼200 Gb of sequencing data are required for 95% abundance-weighted average coverage of the soil communities analyzed. AVAILABILITY AND IMPLEMENTATION: Nonpareil is available at https://github.com/lmrodriguezr/nonpareil/ under the Artistic License 2.0.
Authors: Alejandro Gonzalez-Martinez; Alejandro Rodriguez-Sanchez; Maria Jesus Garcia-Ruiz; Francisco Osorio; Jesus Gonzalez-Lopez Journal: Environ Sci Pollut Res Int Date: 2015-12-09 Impact factor: 4.223
Authors: Xueju Lin; Malak M Tfaily; Stefan J Green; J Megan Steinweg; Patrick Chanton; Aopeau Imvittaya; Jeffrey P Chanton; William Cooper; Christopher Schadt; Joel E Kostka Journal: Appl Environ Microbiol Date: 2014-03-28 Impact factor: 4.792
Authors: Chengwei Luo; Luis M Rodriguez-R; Eric R Johnston; Liyou Wu; Lei Cheng; Kai Xue; Qichao Tu; Ye Deng; Zhili He; Jason Zhou Shi; Mengting Maggie Yuan; Rebecca A Sherry; Dejun Li; Yiqi Luo; Edward A G Schuur; Patrick Chain; James M Tiedje; Jizhong Zhou; Konstantinos T Konstantinidis Journal: Appl Environ Microbiol Date: 2013-12-27 Impact factor: 4.792
Authors: Alexandra Meziti; Despina Tsementzi; Luis M Rodriguez-R; Janet K Hatt; Hera Karayanni; Konstantinos A Kormas; Konstantinos T Konstantinidis Journal: ISME J Date: 2018-11-05 Impact factor: 10.302
Authors: Brittany Suttner; Eric R Johnston; Luis H Orellana; Luis M Rodriguez-R; Janet K Hatt; Diana Carychao; Michelle Q Carter; Michael B Cooley; Konstantinos T Konstantinidis Journal: Appl Environ Microbiol Date: 2020-03-02 Impact factor: 4.792