Dr. P.Schloss,
We are trying to analyze the ion torrent data of amplicon sequencing. The files generated by the sequencer are SFF and FASTQ, which can be used for further analysis. We are following the SOP and the analysis examples provided on your site, but we are facing certain problems as the files available are different than the 454 pyrosequencer. It would be very helpful to us if you create a separate protocol for the ion torrent data analysis. Thank you.
We’re on it. My understanding and preliminary look at IonTorrent data is that it is of a much lower quality than 454 data.
Pat
Dr. Schloss,
Thanks for the reply. According to my knowledge, the data generated by the ion torrent is screened with the threshold of Q20 average value and the sequences are clubbed together in the FASTQ file. We used the command fastq.info to generate the fasta and qual files. Later, in the trim.seqs step, we tried to use the same fasta file with the qaverage=20. But i doubt that the value given by us is appropriate (as compared to the ALGORITHMS used in pyrosequencing data analysis). Also we dint use the oligos, bdiffs and pdiffs parameters as the fasta file generated by the sequencer doesn’t include the bacrcode and primer sequences. Please suggest.
Thanking you. 
Dr. Schloss,
I would also like to ask you a suggestion regarding the ion torrent data analysis that, should we rely on the FASTQ file generated by the sequencer or shall we use the SFF file and start the analysis from scratch?
Thank you
Shreyas.
Dr. Schloss,
We are trying to analyze the amplicon data from Ion Torrent. My doubt is regarding the trimming of the sequences using the trim.seqs command. The qaverage value we are using is ‘15’ and ‘20’, but i am unaware of the differences in the algorithms used for quality check (quality trimming) in the pyrosequencers (454) and in Ion torrent, so any suggestions on this task would be highly appreciated by us. Thanking you.
Shreyas :)