You can use QIIME. Its free and all the codes are publicly available.

You can use QIIME. Its free and all the codes are publicly available.

There are two frequently used free software packages available. One is QIIME (http://qiime.org/) as pointed out by Emine and another one is mothur (https://www.mothur.org/). While I prefer mothur they both have their advantages and disadvantages as described in this nice blogpost http://blog.mothur.org/2016/01/12/mothur-and-qiime/

You can use QIIme, always complemented with other tools (cutadapt, UCHIME, Acacia etc). CLC workbench has also aMicrobial Genomics Module. However is not free and at the end is a black box where you don't know, what exactly the program did. However, If you want the command line codes, I strongly recommend this:

 https://www.ncbi.nlm.nih.gov/pubmed/?term=Assessing+Bacterial+and+Fungal+Diversity+in+the+Plant+Endosphere

This paper has all the codes and might be what you need. 

Thank you all, for your kind answers. The information was very helpful.

with my kind regards and appreciates,

koray

Hi Koray,

I recommend you use the UPARSE pipeline that has been shown to perform better than QIIME especially for de novo assembly. The Nature methods paper is a must read any way.

http://www.nature.com/nmeth/journal/v10/n10/full/nmeth.2604.html

If you dont want to use command line then you can use our online implementation of UPARSE that is fast and installation free at:

https://www.imngs.org

Just register and select the analysis tab and upload your fastq files (as a study). In an hour or so you will receive a mail that your OTU table is finished and you can download it.

For post OTU table, downstream analysis (alpha beta diversity, statistics correlations etc.) we release a set of R scripts called Rhea. You dont need any R knowledge to run them as everything is already formulated. The manuscript will appear beginning of January in PeerJ, but you can already download the scripts and use them from GitHub

https://lagkouvardos.github.io/Rhea/

If you have any question about using our tools do not hesitate to ask.

All the best,

Ilias