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[DESCRIPTION]
<p>Commands for hands-on component of QIIME, which should be run from a local installation. Details can be found online at http://qiime.org/install/index.html.</p>
<p> </p>
<p>The files used in this hands-on component are also available the virtual machine (details in 'Start Instructions'), but you will need to upload them to your Google Drive or Dropbox from within the VM in order to have them available for QIIME, which is installed locally.</p>

[BEFORE_START]
<p>Before starting, please visit the ECOGEO website for more information on this "Introduction to Environmental 'Omics" training series. The site contains a pre-packaged virtual machine that can be downloaded and used to run all of the protocols in this protocols.io collection. In addition to the VM, the website contains video and presentations from our initial "Intro to Env 'Omics" workshop held at the Univ. of Hawai'i at Manoa on 25-26 Jul 2016.<br /><br />Please email ‘ecogeo-join@earthcube.org’ to join the ECOGEO listserv for future updates.</p>

[GUIDELINES]
<p>1. Filter low sequence count samples from table (minimum sequence count: 7500)</p>
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<div data-canvas-width="180.80278075649989">$ filter_samples_from_otu_table.py -i denovo_otu.biom -o core_diversity7500/table_mc7500.biom -n 7500</div>
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<div data-canvas-width="8.195135046">2. Rarify the OTU table to 7500 sequences/sample</div>
<div data-canvas-width="211.6897614675269">$ single_rarefaction.py -i core_diversity7500/table_mc7500.biom -o core_diversity7500s/table_even7500.biom -d 7500</div>
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<div data-canvas-width="118.20538885050001">3. Beta Diversity (weighted_unifrac)</div>
<div data-canvas-width="208.30404989100006">$ beta_diversity.py -i core_diversity7500s/table_even7500.biom -o core_diversity7500/bdiv_even7500/ --metrics weighted_unifrac -t ref_set.tre</div>
<div data-canvas-width="138.79760616749996"> </div>
<div data-canvas-width="138.79760616749996">4. Principal coordinates (weighted_unifrac)</div>
<div data-canvas-width="292.276218062896">$principal_coordinates.py -i core_diversity7500/bdiv_even7500//weighted_unifrac_dm.txt -o core_diversity7500/bdiv_even7500//weighted_unifrac_pc.txt</div>
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<div data-canvas-width="135.26950554599995">5. Make emperor plots, weighted_unifrac)</div>
<div data-canvas-width="273.1662619582867">$make_emperor.py -i core_diversity7500s/bdiv_even7500//weighted_unifrac_pc.txt -o core_diversity7500/bdiv_even7500//weighted_unifrac_emperor_pcoa_plot/ -m map_file.txt</div>
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<div data-canvas-width="65.707899852">6. Alpha rarefaction</div>
<div data-canvas-width="233.74972960500006">$ multiple_rarefactions.py -i core_diversity7500/table_mc7500.biom -m 10 -x 7500 -s 749 -o core_diversity7500/arare_max7500//rarefaction/</div>
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<div data-canvas-width="134.085375420381">7. Alpha diversity on rarefied OTU tables</div>
<div data-canvas-width="220.1165894550002">$ alpha_diversity.py -i core_diversity7500/arare_max7500//rarefaction/ -o core_diversity7500_1105noblanks/arare_max7500//alpha_div/ -t ref_set.tre</div>
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<div data-canvas-width="53.216972229456">8. Collate alpha</div>
<div data-canvas-width="206.24587481400025">$ collate_alpha.py -i core_diversity7500/arare_max7500//alpha_div/ -o core_diversity7500_/arare_max7500//alpha_div_collated/</div>
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<div data-canvas-width="99.09537679649996">9. Rarefaction plot: All metrics</div>
<div data-canvas-width="217.21417463550023">$ make_rarefaction_plots.py -i core_diversity7500/arare_max7500//</div>
<div data-canvas-width="60.629599911300005">alpha_div_collated/ -m 150701_CAWSMF_1104.txt -o core_diversity7500/arare_max7500//alpha_rarefaction_plots/</div>
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<div data-canvas-width="86.586032666007">10. Summarize Taxonomy</div>
<div data-canvas-width="228.83418719700026">$ summarize_taxa.py -i core_diversity7500s/taxa_plots/table_mc7500_sorted.biom -o core_diversity7500/taxa_plots/</div>
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