Question: Quality control for Ion Torrent
0
gravatar for erwan.scaon
2.1 years ago by
erwan.scaon580
Limoges - CBRS - France
erwan.scaon580 wrote:

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 • 2.0k views
ADD COMMENTlink modified 2.1 years ago by Medhat8.0k • written 2.1 years ago by erwan.scaon580
1

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.

ADD REPLYlink written 2.1 years ago by genomax59k

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

ADD REPLYlink written 2.1 years ago by 5heikki7.9k
3
gravatar for Medhat
2.1 years ago by
Medhat8.0k
Poland
Medhat8.0k wrote:

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

ADD COMMENTlink modified 13 months ago • written 2.1 years ago by Medhat8.0k
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