Table 1 A list of resources

Tutorial

http://www.microbio.me/qiime/docs/tutorials/tutorial.html

Examples available at: http://www.microbio.me/qiime/

Register (free, 2-minute process) then retrieve hundreds of examples.

Tools

‘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:

QIIME forum: https://groups.google.com/forum/#!forum/qiime-forum

Mothur: http://www.mothur.org/wiki/Main_Page

SeqAnswers: http://seqanswers.com/forums/index.php

StackExchange: http://biology.stackexchange.com/

Local clusters

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/

Sample collection and processing protocols, bioinformatics pipelines and technical information

EMP: http://www.earthmicrobiome.org/emp-standard-protocols/

HMP: http://www.hmpdacc.org/

QIIME/Mothur workshops online as above, and distance workshops such as:

STAMPS: http://hermes.mbl.edu/education/courses/special_topics/stamps.html

QIIME tutorials: https://www.qiime.org/tutorials

Software Carpentry: http://software-carpentry.org/

NGS overviews: http://informaticstraining.hms.harvard.edu/

Open courses

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