| dc.contributor.author | Konstantinidis, Kostas | |
| dc.contributor.author | Rodriguez, Luis M. | |
| dc.coverage.temporal | June 2012 - July 2012 | |
| dc.date.accessioned | 2014-02-14T14:10:01Z | |
| dc.date.available | 2014-02-14T14:10:01Z | |
| dc.date.issued | 2014-02-03 | |
| dc.identifier.citation | Rodriguez-R LM, Konstantinidis KT. (2013). Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets. Bioinformatics btt584. doi: 10.1093/bioinformatics/btt584 | en_US |
| dc.identifier.uri | http://hdl.handle.net/1853/50889 | |
| dc.description | The files provide simulated metagenomic datasets, generated in silico from complete bacterial and archeal genomes. The read length and frequency of errors are based on Illumina technology. The objective of these simulated datasets was to evaluate the performance of Nonpareil, an algorithm and implementation designed to estimate the average coverage of metagenomic datasets. Nonpareil is described in the following publication: Abstract is from related publication, Rodriguez-R LM, Konstantinidis KT. (2013). Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets. Bioinformatics btt584. doi: 10.1093/bioinformatics/btt584.
Nonpareil, the method described in the related publication, which was tested using these data, can be found at https://github.com/lmrodriguezr/nonpareil/ under the Artistic License 2.0. | en_US |
| dc.description | These files are part of a larger collection of in silico metagenomic samples, derived from all complete bacterial and archeal genomes in NCBI’s GenBank. In order to recreate the full collection, please also see the additional tiers of files, All Complete Bacterial and Archeal Genomes -- Set 1, 2, 3, 4, 5, and 7. Each tier contains one "README.txt" file in raw text format, as well as paired files with the same prefix. Those files ending with ".fa.gz" are the sequences of the simulated dataset in the FastA/gzipped format, and those files ending with ".genomes" are the tables of abundance per molecule. All files are packaged in a zipped file, and may need to be extracted before they can be used. | en_US |
| dc.description.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. Due 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, OTU 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 about 200Gb of sequencing data are required for 95% abundance-weighted average coverage of the soil communities analyzed. | en_US |
| dc.description.sponsorship | United States. Department of Energy | en_US |
| dc.description.sponsorship | National Science Foundation (U.S.) | en_US |
| dc.language.iso | en_US | en_US |
| dc.publisher | Georgia Institute of Technology | en_US |
| dc.relation.ispartofseries | Metagenomic Datasets Simulated In Silico for the Evaluation of Nonpareil | |
| dc.relation.uri | http://hdl.handle.net/1853/50763 | |
| dc.relation.uri | http://hdl.handle.net/1853/50835 | |
| dc.relation.uri | http://hdl.handle.net/1853/50839 | |
| dc.relation.uri | http://hdl.handle.net/1853/50765 | |
| dc.relation.uri | http://hdl.handle.net/1853/50766 | |
| dc.relation.uri | http://hdl.handle.net/1853/50888 | |
| dc.rights | These data were collected from the National Center for Biotechnology Information (NCBI) database GenBank, which was designed to provide and encourage access within the scientific community to sources of current and comprehensive information. NCBI and Georgia Tech place no restrictions on the use or distribution of the data contained in this collection. However, some of the original data may be subject to patent, copyright, or other intellectual property rights. Neither NCBI nor Georgia Tech are in a position to assess the validity of such claims and since there is no transfer or rights from submitters to NCBI, NCBI has no rights to transfer to a third party. For more information on NCBI's copyright disclaimer, please see: http://www.ncbi.nlm.nih.gov/About/disclaimer.html | |
| dc.subject | Environmental and clinical microbiology | en_US |
| dc.subject | Bioinformatics applications | en_US |
| dc.subject | Sequence analysis | en_US |
| dc.subject | Metagenomics | en_US |
| dc.subject | Operational taxonomic units | en_US |
| dc.subject | Nonpareil | en_US |
| dc.title | All Complete Bacterial and Archeal Genomes -- Set 6 | en_US |
| dc.type | Dataset | en_US |
| dc.contributor.corporatename | Georgia Institute of Technology. School of Civil and Environmental Engineering | en_US |
| dc.contributor.corporatename | Georgia Institute of Technology. School of Biology | en_US |
| dc.embargo.terms | null | en_US |
