How can I analyse NGS data of microbiome (For beginner)?

Question

[Sequencer]

I am beginner in the field of Bioinformatics and started analysing NGS data of microbiome. I would like to know from where shall I start. 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 (How to analyse data from start to prparing graphs).

Thank you.

[Carambakaracho]

maybe Daniel Huson's MEGAN might be something to start with (MEGAN6 available here). Anyway it'll be a bumpy road, afaik qiime, megan are the best programs where the user needs to develop the least. You might look into MG-RAST, but I won't provide a link as I have too much reservations in the algorithms behind it.

[ctseto]

qiime2.org has a decent tutorial for the OTU table generation and the like. As you're starting out, may want to pick up toy data and run with it first; as tempting as it is to throw your real data into the mix, the more confident/familiar/competent you are with your data, the less "oops, gotta change elements of the pipeline and start over" (been there more times than I want to admit) there will be.

Answer 1

[lakhujanivijay]

Look at this old post A: How do i should proceed with 16S rRNA amplicon sequencing data from Illumina MiS