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Quality control for Ion Torrent

Is there a tool to check the quality of ion torrent fastq files ?

Something like FastQC, but designed for ion torrent and not for Illumina (since running FastQC on ion torrent data always raise more "red flags" than it should)

sequencing
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updated by Medhat Medhat • written by erwan.scaon erwan.scaon

You can change intervals that raise the "red flags" in FastQC, if they bother you. Edit those settings in limits.txt file that can be found in the Configurations folder.

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written by GenoMax GenoMax

Torrent Server does QC for you and there should be no need for anything else. What are you seeing with FastQC?

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written by 5heikki 5heikki

1 answer

you can try ClinQC from this paper they put in mind Ion torent

We have developed ClinQC, a flexible and user-friendly pipeline for format conversion, quality control, trimming and filtering of raw sequencing data generated from Sanger sequencing and three NGS sequencing platforms including Illumina, 454 and Ion Torrent

Good luck

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written by Medhat Medhat

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