The latest Illumina sequencers muddle samples
The new Illumina patterned flow cell technology uses chemistry that is prone to “index hopping”, leading to reads being assigned to the wrong sample in multiplexed sequencing runs. This problem has already caused countless research groups to re-assess their experimental results or refrain from using the new sequencers. However, with careful experimental preparation it may be possible to ameliorate this situation so as to become negligible for most applications
