Integrative Biology & Medicine ~ IntegrativeBio
Description: Articles written about common next-generation sequencing problems experienced by bioinformaticians.
biology (980) dna (816) ngs (129) next generation sequencing (56) qc fail qcfail quality control fail
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
June 7, 2017 Steven Wingett HiSeq , Illumina , X Ten , All Applications
The latest Illumina sequencers – such as the HiSeq X, HiSeq 3000 and HiSeq 4000 – use patterned flow cells to enable the discrimination between much more densely packed DNA clusters. While such technology substantially increases the number of reads generated per sequence run, this innovation may lead to an increased number of duplicates, thereby negating the improved yield and making subsequent data analysis potentially more difficult. Further investigation shows that these putative sequencing duplicates ar
Integrative Biology & Medicine ~ IntegrativeBio