Earth Microbiome Project
The Earth Microbiome Project (EMP) is a systematic attempt to characterize the global microbial taxonomic and functional diversity for the benefit of the planet and mankind.
The EMP is open science: anyone can get involved. The EMP data set is generated from samples that individual researchers have compiled and donated to the EMP. These data sets represent individual EMP studies. In addition to the individual studies, we are performing a cross-study meta-analysis. All per-study raw data is publicly available in the EMP portal to the QIIME database. This repository contains the processed, combined (i.e., across study) EMP data for the EMP meta-analysis as well as code developed specifically for the EMP meta-analyses, and new results as they are generated.
If you're interested in getting involved in EMP data analyses you should begin by reviewing the open issues. These describe analyses that we're interested in performing across studies. If you're interested in working on one of these analyses, or have ideas for other analyses that should be performed, you should get in touch with Greg Caporaso (email@example.com), the Chief Data Analyst for the EMP.
Additional information is available on the Earth Microbiome Project website.
Organization of this repository
data/data files used for downstream analysis (biom tables, trees, mapping files, etc)
data-urls.txtURLs where large data files can be found (e.g., BIOM and tree files). These are not stored in the repository, due to space limitations. You can download all of these files by running
wget -i data-urls.txtfrom this directory.
emp-or.tre.gznewick-formatted tree corresponding to open reference (or) biom table
emp-or-mc2.biom.gzopen-reference (or) biom table
emp-or-mc2-w-tax.biom.gzopen-reference (or) biom table with taxonomy assignments
emp-or-mc2-w-tax-no-pynast-failures.biom.gzopen-reference (or) biom table with taxonomy assignments, not including the OTUs failed to align using PyNAST
emp-cr.biom.gzclosed-reference (cr) biom table
refseqs.fna.gzthe new reference sequence collection resulting from open reference (or) OTU picking
sample-map.txt.gzsample metadata (i.e., mapping) file for all samples in biom table
observation-map.txt.gzobservation (OTU) metadata (e.g., taxonomy assignments) for open reference (or) biom table
codecode developed for EMP analysis
resultshigh-level results (e.g., figures, etc that are useful for presentations)
presentationscollection of presentations on EMP
File name abbreviation conventions
orrefers to open-reference OTU picking
crrefers to closed-reference OTU picking
refseqsrefers to reference sequence collections that could be used in reference-based OTU picking
mc2refers to minimum sequence count in an OTU to be included equals to 2
Finding older data
If you're looking for data generated and used for the ISME 14 EMP presentations, see here.