how to detect contamination or sample preparation artifacts in sequencing results

[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?

[JackieBadger]

http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/

[roll]

http://www.bioinformatics.babraham.a.../fastq_screen/

Thanks. I start using this and now it complaints about libraries.

No search libraries were configured at /Downloads/fastq_screen_v0.4.2/fastq_screen line 119.

I assume it refers to the contamination list. I have the cocntaminant file from the fastQC but it is not clear to me where to mention this list.

I use the following line in my conf file.

DATABASE Adapters /Volumes/bowtie2_index/

Can you please advise if by library it means contamination list and where i should mention the libraries?