shhh.flows for Ion Torrent

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Hi Pat and Sarah,

The answer to this question may be a simple ‘no’ but I was wondering if it at all possible to run shhh.flows on Ion Torrent data? I have some IT data that is in the form of an sff and I have been able to extract a fasta, qual and low file from this. Looking at the flow file there appear to be 520 flows. I was wondering how the .pat lookup files are made? Is it possible to make one for IT and use this to denoise the data?

I have run the data by using only trim.seqs but I’d like to be able to properly denoise the data and maybe not throw out as many reads as I lost with a qaverage threshold of 25 (around 60%)

Apologies if this is a stupid question!
Thanks,
Tris

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In theory it’s possible - but the *.pat files are reformatted verisons of the *.dat files from Chris Quince for 454 data. I imagine that the distributions would be different for IT. Maybe check with Chris and see if he has anything yet?