Question: Quality control for Ion Torrent
0
gravatar for erwan.scaon
19 months ago by
erwan.scaon540
Limoges - CBRS - France
erwan.scaon540 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 • 1.5k views
ADD COMMENTlink modified 19 months ago by Medhat7.6k • written 19 months ago by erwan.scaon540
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 19 months ago by genomax49k

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

ADD REPLYlink written 19 months ago by 5heikki7.3k
3
gravatar for Medhat
19 months ago by
Medhat7.6k
Poland
Medhat7.6k 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 7 months ago • written 19 months ago by Medhat7.6k
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