Have you ever heard of Qiime / Mothur / Dada2? Google it.

Dear Singh, thanks, but i haven't more expertise in metagenomics data analysis, please you can guide me.

Hi,

Please try to use Mothur/Qiime.

For Mothur, you can refer to the url below which gives a full SOP for analyzing Miseq data.If yours is from 454 you can navigate to the respective SOP.

https://www.mothur.org/wiki/MiSeq_SOP

Hope that helps

Thanks

Dear Sandipan Samaddar @

You know about something pipeline for metgenomics data analysis (adapter remove, QC control, assembly, annotation, extraction of single genomes, resistor prediction, abundance, another analysis) ?

I would recommend you to first decide what you want to do... You are asking so many questions but they are just random nothing specific...

I'll second Abhijeet.

Your original question asked about 16S rRNA metgenomics, i.e. metabarcoding, or amplicon sequencing. Your clarification seems to suggest you have data/want to do shotgun metagenomics. Assembly, annotation, extraction of genomes etc. have no place in a metabarcoding analysis.

Very brief (and not exhaustive) descriptions:

Metabarcoding (rRNA) will typically be used for investigating species diversity and their abundance.

Shotgun metagenomics (DNA) can also give an estimate of species diversity. It can also estimate the functional potential of a microbiome. You may also get full genomes for some of the resident species.

Metatranscriptomics (RNA) is in effect RNA-seq of a microbiome - it measures transcription within a microbiome.