Journal article Open Access

A communal catalogue reveals Earth's multiscale microbial diversity

Thompson, Luke R.; Sanders, Jon G.; McDonald, Daniel; Amir, Amnon; Navas, Jose; Kopylova, Evguenia; Ackermann, Gail


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{
  "DOI": "10.5281/zenodo.890000", 
  "abstract": "<p><strong>Overview</strong></p>\n\n<p>This archive contains data and results from the meta-analysis of the Earth Microbiome Project (EMP) 16S Release 1, which was published in <em>Nature</em> (http://doi.org/10.1038/nature24621). The files include\u00a0EMP-wide study and sample metadata, observation tables and information (trees and taxonomies), alpha- and beta-diversity results, observation summaries for trading cards, and\u00a0the Redbiom database at time of publication.</p>\n\n<p><strong>Files</strong></p>\n\n<p>* Study metadata<br>\n\u00a0 \u00a0 - emp_studies.csv<br>\n* Sample metadata<br>\n\u00a0 \u00a0 - emp_qiime_mapping_release1_20170912.tsv<br>\n\u00a0 \u00a0 - emp_qiime_mapping_qc_filtered_20170912.tsv<br>\n\u00a0 \u00a0 - emp_qiime_mapping_subset_10k_20170912.tsv<br>\n\u00a0 \u00a0 - emp_qiime_mapping_subset_5k_20170912.tsv<br>\n\u00a0 \u00a0 - emp_qiime_mapping_subset_2k_20170912.tsv<br>\n* Observation tables (.biom) and summaries (.summary.txt)<br>\n\u00a0 \u00a0 - emp_deblur_90bp.release1.biom<br>\n\u00a0 \u00a0 - emp_deblur_90bp.release1.summary.txt<br>\n\u00a0 \u00a0 - emp_deblur_100bp.release1.biom<br>\n\u00a0 \u00a0 - emp_deblur_100bp.release1.summary.txt<br>\n\u00a0 \u00a0 - emp_deblur_150bp.release1.biom<br>\n\u00a0 \u00a0 - emp_deblur_150bp.release1.summary.txt<br>\n\u00a0 \u00a0 - emp_cr_gg_13_8.release1.biom<br>\n\u00a0 \u00a0 - emp_cr_gg_13_8.release1.summary.txt<br>\n\u00a0 \u00a0 - emp_cr_silva_16S_123.release1.biom<br>\n\u00a0 \u00a0 - emp_cr_silva_16S_123.release1.summary.txt<br>\n\u00a0 \u00a0 - emp_or_gg_13_8.no_sample_singletons.biom<br>\n\u00a0 \u00a0 - emp_or_gg_13_8.no_sample_singletons.summary.txt<br>\n* Observation information (sequences, trees, taxonomies)<br>\n\u00a0 \u00a0 - emp_observation_info_deblur.tar.gz<br>\n\u00a0 \u00a0 - emp_observation_info_cr_gg.tar.gz<br>\n\u00a0 \u00a0 - emp_observation_info_cr_silva.tar.gz<br>\n\u00a0 \u00a0 - emp_observation_info_or_gg.tar.gz<br>\n* Alpha-diversity results<br>\n\u00a0 \u00a0 - emp_alpha_div.tar.gz<br>\n* Beta-diversity results<br>\n\u00a0 \u00a0 - emp_deblur_unifrac_dist.tar.gz<br>\n\u00a0 \u00a0 - emp_deblur_unifrac_pc.tar.gz<br>\n\u00a0 \u00a0 - emp_deblur_unifrac_emperor.tar.gz<br>\n\u00a0 \u00a0 - emp_90_gg_1k_unweighted_unifrac.txt.gz<br>\n\u00a0 \u00a0 - emp_150_gg_1k_unweighted_unifrac.txt.gz<br>\n* Observation summaries for trading cards<br>\n\u00a0 \u00a0 - otu_summary.emp_deblur_90bp.subset_2k.rare_5000.tsv<br>\n\u00a0 \u00a0 - otu_summary_no_chl.emp_deblur_90bp.subset_2k.rare_5000.tsv<br>\n\u00a0 \u00a0 - emp_2k_subset_blank_stats.tsv<br>\n* Redbiom database<br>\n\u00a0 \u00a0 - emp_redbiom.rdb</p>", 
  "author": [
    {
      "family": "Thompson, Luke R."
    }, 
    {
      "family": "Sanders, Jon G."
    }, 
    {
      "family": "McDonald, Daniel"
    }, 
    {
      "family": "Amir, Amnon"
    }, 
    {
      "family": "Navas, Jose"
    }, 
    {
      "family": "Kopylova, Evguenia"
    }, 
    {
      "family": "Ackermann, Gail"
    }
  ], 
  "container_title": "Nature", 
  "id": "890000", 
  "issued": {
    "date-parts": [
      [
        2017, 
        11, 
        1
      ]
    ]
  }, 
  "language": "eng", 
  "note": "This work was supported by the John Templeton Foundation (grant ID 44000, Convergent Evolution of the Vertebrate Microbiome), the W. M. Keck Foundation (DT061413), Argonne National Laboratory (US Dept. of Energy contract DE-AC02-06CH11357), the Australian Research Council, and the Extreme Science and Engineering Discovery Environment (XSEDE, project number BIO150043), which is supported by National Science Foundation grant number ACI-1053575. We thank MO BIO Laboratories, Luca Technologies, Eppendorf, Boreal Genomics, Illumina, and Roche for in-kind support at various phases of the project.", 
  "publisher": "Zenodo", 
  "title": "A communal catalogue reveals Earth's multiscale microbial diversity", 
  "type": "article-journal"
}
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