17th Jun, 2015
Case Western Reserve University
Question
Asked 10th Jun, 2015
How can I analyse NGS data of microbiome (For beginner)?
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.
Most recent answer
Thank you for sending me link for the book. I will certainly look into it.
Asifa
All Answers (11)
I had similar feeling in the begging but I think you can use lot of web source. If you are starting with Qiime, there is this basic turtorail
and some basic commands can be looked in
These links helped me a lot and of course you will learn a lot when you start to analyse your own data.
1 Recommendation
11th Jun, 2015
Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO)
I perfectly agree, I suggest you to start reading Linux for beginners manuals, and step by step entering in bioinformatics.
If you are going to analyze 16S rDNA sequences, RDP project (http://rdp.cme.msu.edu/) hase a very good pipeline for taxonomic assignation.
For metagenomics you can have a loot at MG-RAST (https://metagenomics.anl.gov/)
I hope this help.
bests
Giuseppe
Thank you Rumakanta and Auria for providing useful resources. I will certainly take help of these resources and if I have specific question. I will come back.
Asifa
Even before deciding if you want to start coding, you might want to take a look at the Galaxy platform: https://usegalaxy.org/
It is a public online platform with a large number of bioinformatics tools, such as the NGS tools you might want to use. No coding knowledge is required, and there are information pages on all the tools within the platform. The computing is done on a queue bassis on their cluster, therefore also removing the need for high performing computer.
There are also available tutorials on Galaxy. It is a great starting point for biologists.
Patricia
1 Recommendation
Hi Asifa,
I made a modified version of the QIIME tutorial with some added explanations, along with some sprinkled in info on the logistics and navigating in the UNIX terminal:
I hope it's helpful, if you haven't seen it already.
Cheers,
Jeff
1 Recommendation
Since everyone else is recommending QIIME, I'll just thrown in another option: in my lab, we use mothur, which I find quite easy to use. The MiSeq SOP is at http://www.mothur.org/wiki/MiSeq_SOP. There's also a forum at http://www.mothur.org/forum/ and the developers are very supportive and quick to answer questions.
1 Recommendation
Thank you so much Velma for introducing to this tool. Before I start reading and get myself familiar with this tool, I am guessing that mother software will work for Mac.
Asifa
Thank you Dr. Werner for sending me the information. I have started working from that site but was finding difficulty to follow. I will check again updated version of tutorial. I guess I am a beginner and not used Unix commands so each and every step takes time to execute. I will get use to it soon suggested by everyone here. Thank you to all.
Maybe a more in-depth unix tutorial would help? Or a book? The O'Reilly books are pretty well-respected and they have one on Unix in OS X http://shop.oreilly.com/product/0636920025870.do
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