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Shot Gun metagenome sequence analysis

Hi everyone,

I am seeking some info related to shotgun metagenomic data analysis. I am a beginner in metagenome analysis.

Recently we did a shotgun metagenome sequencing for few of my samples. we did through Iontorrent sequencing. I want to extract only 16S rRNA gene sequences from metagenome to compare with my amplicon sequencing data.

Does anyone please tell me the programs/ software/ scripts to do the same. I have tried with mothur but i had no luck. Any help will be much appreciated.

Thanks and regards Venkat

next-gen genome assembly sequencing
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updated by GenoMax GenoMax • written by venkateshbiotech • venkateshbiotech

I have tried with mothur but i had no luck

That tells us very little. What did you try and why do you think you had no luck?

If you are looking to extract only 16s rRNA should you not be looking at something like blast against the 16s RNA database?

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written by GenoMax GenoMax

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