Fastest and memory efficient tool for 16S RNA counts
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7.1 years ago
bioinfo ▴ 830

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?

16s rRNA metagenome • 2.0k views
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Hi there,
by raw WGS data, do you mean FastQ file from NGS? Or you already processed your data?

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Its Fastq files from NGS.

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7.1 years ago
glihm ▴ 650

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.

 

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