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?
By raw WGS data, do you mean FastQ file from NGS? Or did you already process your data?
It's Fastq files from NGS.
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! ;)
Another 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.
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