PhiX contamination

[MoritzF]

We recently sequenced a couple bacterical genomes on our MiSeq after making Nextera XT libraries. After assembling we discovered a PhiX-Sequence containing contig within an assembly. We wonder if this might be contamination.

Has anyone else discovered PhiX reads among de-multiplexed reads from a MiSeq Run?

[GenoMax]

Re-reading your post leads me to conclusion that you are referring to the demultiplexing not working correctly on MiSeq leaving some phiX contamination. There was a past thread on this. Here is that thread: http://seqanswers.com/forums/showthread.php?t=26701 Post #8 onwards.

[NextGenSeq]

The lab spiked PhiX into your library. This is usually spiked in at 2%.

[mcnelson.phd]

PhiX contamination in demultiplexed MiSeq datasets is a pretty common thing. It results primarily from image registration errors that cause phiX reads to be incorrectly assigned an index sequence.

Best practice to avoid having these reads cause assembly artifacts is to map your reads against the phiX genome prior to assembly.