Ion torrent sequences analysis

I am new to QIIME. I am planning to use QIIME2. I was checking the moving tutorial experiment tutorial. My sequences were obtained from Iontorrent PGM machine. I have multiplexed fastq file. I can creat meta data file too. But i dont have barcode fastq file. I am wondering how to proceed further in this case?

Hi @anbu_arun,
Do you know where your barcode sequences if you don’t have a separate barcode fastq.gz file? If they’re in your sequence records, you might need to use another tool, like QIIME 1’s to create a separate barcodes file.

Also, note that at this time we don’t have support for quality control of IonTorrent data. This is something we will likely support in the future, but the two quality control pipelines that we do currently support (DADA2 and Deblur) are both Illumina-specific.


Hi @gregcaporaso,
Thank you for your kind reply. My bar-codes are embedded in my main sequence file. As far as i know, the iontorrent output always like that. I will try to use the QIIME 1 for extracting the barcode files.

Please develop develop a tutorial for the ion-torrent sequence analysis as soon as possible. It will benefit the small labs who are all forced to use ion-torrent to save money and keep getting some data.


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