Can anyone suggest me a tool for detecting and quantifying 16S rRNA/rDNA sequences from raw WGS metagenome? I just want to count the number of 16S sequences present in a list of metagenomes quickly. Which software is the fastest nowadays?
What you have, are some pipelines to identify and assign a taxonomy for 16SRNA. For example, QIIME and MOTHUR are the most popular, using USEARCH to realize clustering (which does not matter for you).
I am working on a software for Metagenomic data, and one of the application is what you are looking for. When its ready, I'll post here again! ;)
An other solution for you, If you are fluent with command line, you can use scripts in order to identify the 16S RNA sequence from you data set.