NovaSeq : 2-color chemistry and Base quality problem

 Because of 2-color chemistry of Nova-seq, base quality of Nova-seq could be worse compared to Hiseq which uses 4-color chemistry

 

On NovaSeq Base Quality 

http://lh3.github.io/2017/07/24/on-nonvaseq-base-quality

 

Illumina 2 colour chemistry can overcall high confidence G bases

https://sequencing.qcfail.com/articles/illumina-2-colour-chemistry-can-overcall-high-confidence-g-bases/

WGS from NovaSeq compared to HiSeq

https://www.reddit.com/r/bioinformatics/comments/93eqjm/wgs_from_novaseq_compared_to_hiseq/ 

 

A first look at Illumina’s new NextSeq 500  ( NextSeq use 2-color chemistry)

http://seqanswers.com/forums/showthread.php?t=40741