Question: Fastest and memory efficient tool for 16S RNA counts
0
gravatar for bioinfo
3.7 years ago by
bioinfo690
EU
bioinfo690 wrote:

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?

metagenome 16s rrna • 1.2k views
ADD COMMENTlink modified 3.7 years ago by glihm590 • written 3.7 years ago by bioinfo690

Hi there,
by raw WGS data, do you mean FastQ file from NGS? Or you already processed your data?

ADD REPLYlink written 3.7 years ago by glihm590

Its Fastq files from NGS.

ADD REPLYlink written 3.7 years ago by bioinfo690
0
gravatar for glihm
3.7 years ago by
glihm590
France
glihm590 wrote:

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.

 

ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by glihm590
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