Question

Fastest and memory efficient tool for 16S RNA counts

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8.7 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 • 2.4k views

ADD COMMENT • link updated 18 months ago by Ram 43k • written 8.7 years ago by bioinfo ▴ 830

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Hi there,

By raw WGS data, do you mean FastQ file from NGS? Or did you already process your data?

ADD REPLY • link updated 18 months ago by Ram 43k • written 8.7 years ago by glihm ▴ 660

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It's Fastq files from NGS.

ADD REPLY • link updated 18 months ago by Ram 43k • written 8.7 years ago by bioinfo ▴ 830

Ram · Answer 1 · 2015-08-22

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.