phiX removal

[lgiloteaux]

Hi all,

Looking for an easy command line to remove phiX sequences using bowtie2 on single-end reads. Do I need to index and where can I get the PhiX sequence?
thanks a lot

[GenoMax]

You can get illumina's version of phiX from iGenomes page: http://support.illumina.com/sequenci...e/igenome.html. That should include bowtie/bowtie2/bwa indexes (I have not checked).

[GenoMax]

You can use BBSplit to bin the phiX sequences out as a simple alternative.

[lgiloteaux]

thanks you very much