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[DESCRIPTION]
In this protocol we will show how to taxonomically profile 20 metagenomic shotgun samples <a href="http://www.nature.com/nature/journal/v486/n7402/full/nature11234.html" target="_blank">Human Microbiome Project</a> (HMP). Specifically, we will look at 10 samples from the buccal mucosa and 10 from the tongue dorsum. Please note these 20 samples are not necessarily an unbiased selection of microbiomes from the over 200 buccal mucosa and tongue dorsum samples generated by the HMP.<br /><br />REQUIREMENTS: <a href="http://bowtie-bio.sourceforge.net/bowtie2/index.shtml" target="_blank">BowTie2</a> installed and in the system path, <a href="http://mercurial.selenic.com/" target="_blank">Mercurial</a>, basic unix commands (wget, tar).<br /><br /><em>The size of the 20 samples (60GBs) can make their download quite slow. For this reason we are also providing the overall output of this protocol (few KBs) available for <a href="https://bitbucket.org/nsegata/metaphlan/wiki/profiled_samples.tar.bz2" target="_blank">download</a> so that one can start the tutorial from <a href="https://www.protocols.io/view/MetaPhlAn-output-merge-and-visualization-d9q95v" target="_blank">MetaPhlAn output merge and visualization</a> if needed.</em>

[BEFORE_START]
We assume you have a basic knowledge of shotgun metagenomics and of Unix-based operating systems (although you should be able to run the pipeline on MacOS and Windows, some commands may require modification). Also, Python &gt;2.6 (but not Python 3) is required to be installed (Python 2.7 for Step 5).

[GUIDELINES]
<p><strong>MetaPhlAn2 is now ready at:</strong><br /><br /></p>
<p><a href="http://segatalab.cibio.unitn.it/tools/metaphlan2/" target="_blank">http://segatalab.cibio.unitn.it/tools/metaphlan2/</a></p>
<p><a href="https://bitbucket.org/biobakery/biobakery/wiki/metaphlan2" target="_blank">https://bitbucket.org/biobakery/biobakery/wiki/metaphlan2</a></p>
<p><a href="https://bitbucket.org/biobakery/metaphlan2" target="_blank">https://bitbucket.org/biobakery/metaphlan2</a><br /><br />This tutorial is also a step-by-step description of the metagenomic pipeline we used in our review paper about <a href="http://www.nature.com/msb/journal/v9/n1/full/msb201322.html" target="_blank">computational meta'omics</a> (specifically <a href="http://www.nature.com/msb/journal/v9/n1/fig_tab/msb201322_F4.html" target="_blank">Figure 4</a>). The references for each tool are reported at the end of this page. If you find these tools useful, we kindly ask you to use these references for citing. Additionally, links to the corresponding user groups are provided should you have any comments or suggestions you would like to share with us.</p>
<p>We assume you have a basic knowledge of shotgun metagenomics and of Unix-based operating systems (although you should be able to run the pipeline on MacOS and Windows, some commands may require modification). Also, Python &gt;2.6 (but not Python 3) is required to be installed (Python 2.7 for Step 5).</p>
<p>Please do not hesitate to contact <a href="mailto:nicola.segata@unitn.it" target="_blank">us</a> if you have any comments, suggestions, or clarification requests regarding the tutorial or if you would like to contribute to this resource. We are also <strong>looking for motivated students and postdocs for developing new metagenomic tools</strong>, check <a href="http://www.unitn.it/en/cibio/28516/laboratory-of-computational-metagenomics" target="_blank">here</a> if you are interested.<br /><br />The commands reported in this protocol can be retrieved as a <a href="https://bitbucket.org/nsegata/metaphlan/wiki/1_metaphlan_profiling.sh" target="_blank">bash script</a>.</p>

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