Remove Illumina Adapters

Question

[K.Nijbroek]

Hi,

I've got mate-paired reads via Illumina HiSeq, and they may contain adapter/primer sequences. Does anyone of you know the best tool which can detect these adapter/primer sequences and remove these from .FASTQ files? Preferable the tool has to work on windows (such as java tools).

I have tried cutadapt but since cutadapt relies on known adapter/primer sequences it won't do the trick (and I didn't manage to get it working on windows).

Thanks,

[Fabio Marroni]

Just out of curiosity: which tool are you then using to align in windows? If you are using some commercial tool maybe they also perform adapter removal. However, as Istvan Albert pointed out, any tool for removing adapters will require you to know adapter sequences.

Answer 1

[Istvan Albert]

Trimmomatic is a good and fast option.

But, every tool will require that you tell it what the adapters are, after all how would these know what to cut off, your samples could have all kinds of systematic sequences in them