Metagenomic Iontorrent reads: filtering and denoising

Question

[fhsantanna]

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.

Answer 1

[5heikki]

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..

Answer 2

[sacha]

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