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Tutorial
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http://www.microbio.me/qiime/docs/tutorials/tutorial.html
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Examples available at: http://www.microbio.me/qiime/
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Register (free, 2-minute process) then retrieve hundreds of examples.
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Tools
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‘Omics’ data requires bioinformatic pipelines: QIIME, Mothur, LEfSe, MetaPhlAn, USEARCH, UPARSE, PandaSeq, and others. They are relatively complicated and non-intuitive, but the following sites are particularly helpful:
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QIIME forum: https://groups.google.com/forum/#!forum/qiime-forum
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Mothur: http://www.mothur.org/wiki/Main_Page
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SeqAnswers: http://seqanswers.com/forums/index.php
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StackExchange: http://biology.stackexchange.com/
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Local clusters
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As ‘Omics’ tools require computational power, it may be feasible to have a local cluster through AWS Educational Grants: http://aws.amazon.com/education/, or partner with a bioinformatics lab such as via Project Rosalind: http://rosalind.info/about/ and Project Euler: http://projecteuler.net/
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Sample collection and processing protocols, bioinformatics pipelines and technical information
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EMP: http://www.earthmicrobiome.org/emp-standard-protocols/
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HMP: http://www.hmpdacc.org/
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QIIME/Mothur workshops online as above, and distance workshops such as:
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STAMPS: http://hermes.mbl.edu/education/courses/special_topics/stamps.html
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QIIME tutorials: https://www.qiime.org/tutorials
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Software Carpentry: http://software-carpentry.org/
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NGS overviews: http://informaticstraining.hms.harvard.edu/
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Open courses
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Open courses are also available: Coursera: https://www.coursera.org/, such as Biostatistics boot camp, Machine learning, Bioinformatics methods with an MIT site being helpful. http://ocw.mit.edu/index.htm
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