I am beginner in the field of Bioinformatics and started analysing NGS data of microbiome. I would like to know what is the best software available to start analzsing sequencing files from MiSeq. I have started using Qiime but I do not know much of UNix command. Is there any book where it is described how to go about it from quality control, attaching barcode, pair end overlapping sequence, and then generation OTU tables and further analysis.

Thank you.

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