I am working on the fish gut microbiome. For the metagenomics study, I already sequence 16S rRNA gene of different types of fish gut samples. After sequencing, I have two reads (R1 and R2) as fastq format. Now, I want to analyze the data. Specifically, I want to analyze the 'beta' diversity of those samples.
As I am a beginner in metagenomics data analysis. For this reason, which will be the simplest method or process for me to analyze 'beta' diversity of those samples? Are there any online tools for 'beta' diversity analysis?
Thank you.
If you have a good computer system with high server configuration QIIME is the best. If the reads are assembled in fasta format you can use comparatively simple software MOTHUR. Both are Linux based
If you have a good computer system with good server configuration QIIME is the best. Otherwise if you assembled the reads in fast format you can use the simple software MOTHUR. Both are Linux based.
Sulav Indra Paul
For your question Sebastian Proost
,has suggested you the best tool available (till data) and good tutorial as well. However, I would suggest you that, if you are a beginner in this kind of analysis, please do not blindly follow the tutorials or any tool/manual/database/etc. without understanding the aim/purpose/basics of related thing and also try to define your aim (what/how/why you want to do).It is also visible by the way you have framed the question that you need basic training in bioinformatics and NGS data sequencing/analysis. So, please try to make your base strong rather than just jumping on using tools and get readymade results (which might not make much sense without theoretical understanding).
Dear Mr. Paul,
I would suggest you to use QIIME pipeline. Obviously, it will take some time to understand the fundamental of Metagenomics and NGS. Butr, it is highly utilized pipeline for NGS data analysis. Furthermore, as per your requirements, you can analyze measures of both alpha-diversity (within sample) and beta diversity (differences between samples) in same pipeline.
use vegan package from R (https://cran.r-project.org/web/packages/vegan/index.html)
I found qiime2 to be quite convenient and have nice tutorial where you can learn. If you still struggling, you can contact me.
I would definitely recommend QIIME2. it is Linux base so you will need some basic knowledge in executing commands. But I agree with Abhijeet Singh , you should do some reading on metagenomics first for a solid foundation.
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