Question: Metagenomic Iontorrent reads: filtering and denoising
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gravatar for fhsantanna
3.5 years ago by
fhsantanna470
Brazil
fhsantanna470 wrote:

I have metagenomic reads generated through iontorrent technology. The library was derived from total DNA extracted from seawater samples.

I have read that before the binning proccess, I must filter and denoise the reads. Which parameters do you recommend for the filtering step? I have utilized a filtering protocol desgined for transcriptome analysis, where the minimum length of the reads should be 30 and the minimum phred score should be 17. What do you think about that? Is it worth for metagenomics? Which software do you recommend for denoising my reads? Thanks.

ADD COMMENTlink modified 3.5 years ago by sacha1.9k • written 3.5 years ago by fhsantanna470
0
gravatar for 5heikki
3.5 years ago by
5heikki8.7k
Finland
5heikki8.7k wrote:

I think Ion Torrent reads are quality controlled automatically by the Torrent Server. Unless you're using the raw output files, you should be fine..

ADD COMMENTlink written 3.5 years ago by 5heikki8.7k
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gravatar for sacha
3.5 years ago by
sacha1.9k
France
sacha1.9k wrote:

I use sickle https://github.com/najoshi/sickle. But check first your reads with fastqc

ADD COMMENTlink written 3.5 years ago by sacha1.9k
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