How To Detect Contamination Or Sample Preparation Artifacts In Sequencing Results

Question

[roll]

Hi,

Is there any tool (apart from fastQC) to detect all primers/adapters(contaminants basically) in my raw fastq file that needs to be removed before mapping?

Answer 1

[arnstrm]

PRINSEQ gives a nice sequence logo using the FASTQ files like this:

You can easily see any contaminating tags.

[roll]

thanks, does this give you statistics or the actual list of contaminants? So that i can use this list to remove them from my data.

[arnstrm]

I think the only statistics that it gives is "Probability of tag sequence" at 5' end and 3' end. What kind of list do you need?