I have used Nextera library kit for the first time and had issues with the reads coming out of HiSeq 100 being GC biased .... but only for the first few base pair reads. The majority of the reads is good. Just wondering if it is a common issue with Nextera kits.
It is common. The transposase that the Nextera kit uses has a GC-insertion bias. I found a good demonstration of this here:
http://openwetware.org/wiki/BioMicroCenter:Nextera
Yes, the Nextera kit has a GC insertion bias. It is documented in ocean phage genomes in Marine et al. 2011, and my group has a new manuscript showing further evaluation of this kit relative to standard library prep methods again demonstrating an insertion bias (Solonenko et al. which will be in review as of Nov 30, 2012).
1. Marine, R., et al., Evaluation of a transposase protocol for rapid generation of shotgun high-throughput sequencing libraries from nanogram quantities of DNA. Applied and Environmental Microbiology, 2011. 77(22): p. 8071-9.
- Badges
- Science method