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