Quality control for Ion Torrent

Question

[erwan.scaon]

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)

[GenoMax]

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.

[5heikki]

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

Answer 1

[Medhat]

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