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We are starting a metagenomics project in our research group to study microbiota in the respiratory tract. Since the are no books yet about metagenomics, seems reading some reviews and online tutorials is the only alternative.

Could you suggest me essential papers, websites or other resources useful for my purpose.

Thanks

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    $\begingroup$ You can have a look at some of the lecture slides of previous years' EBI-Metagenomics course. $\endgroup$ – WYSIWYG Nov 18 '14 at 11:45
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The Coursera Bioinformatic Methods courses include classes on metagenomics and, more importantly, tools to use when applying these methods. I have not taken this particular course, but Coursera is generally very good with getting hands-on experience using computational tools. A course-like setting may also be conducive to group learning.

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In the paper here compared lots of different tools for the different parts of the anlysis in metagenomics. It is a comprehensive study in which several labs participated.

You need to take into account that not necessarily the most popular tools are the best. And in the end it will depend on what you want to and how you do it.

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