What are the suitable software to analyze the 16S raw DNA sequences for microbial diversity analysis ?

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Wiwiek Harsonowati

please read about DADA2, QIIME2, Mothur, MG-RAST, Galaxy server, Unipro Ugene, BioEdit and choose according your need/expertise

Vincent Mulholland

For a quick look at the data you could try the Kaiju web server: http://kaiju.binf.ku.dk/

You submit a compressed FASTA or FASTQ file. The analysis gives detailed output files in a format you can import into Excel. One also gets an interactive Krona chart, which allows you to zoom in to various taxonomic levels. Really quick results compared to other methods, but probably not publication quality by itself.

Salvador Ramirez-Flandes

The term "analyze" without indicating at least one objective does not say very much. That depends a lot on what you want to do. What are your hypotheses about your data for example? ok, if you are not an hypothesis-driven researcher then at least you must have some ideas on mind because otherwise you will be quite lost looking at some very different ways to look the data through the different software that we might recommend you. In fact, I would not recommend any sophisticated software for this but to go step by step. On a first approach I would try to recognize a suitable reference database to compare your sequences against to. ARB-Silva for example is a good start (other are greengenes and rdp). This comparison is typically done using BLAST (or any other high-performance replacement, like vsearch or usearch). Then you will have at least a taxonomic structure for your data and then you can start asking more question to your data.

I hope that helps.

----sram

Marwan E Majzoub

Galaxy will help you analyse and it is quite straight forward to use

No need for high computing resources

Mehrdad Rabiei

Hi sir and colleagues,

Could you please give me some info regarding Galaxy?

Could you also please share its link?

By the way, do you know how possible to analyze microbial functional genes' reads (such as dsrB, mcrA)? (no taxonomy reference and sequence reference unlike 16S rRNA, e.g. SILVA)

Thanks a lot

Prachi Singh

Hi,

Can I use MG_RAST for the analysis of the 16S rRNA PCR product? Even for functional genes?

Thank you!