A recent paper from Mike Quail's group at the Sanger Institute compares 9 different library prep kits for WGS. In Quantitation of next generation sequencing library preparation protocol efficiencies using droplet digital PCR assays - a systematic comparison of DNA library preparation kits for Illumina sequencing, the authors used a digital PCR (ddPCR) assay to look at the efficiency of ligation and post-ligation steps. They show that even though final library yield can be high, this can mask poor adapter ligation efficiency - ultimately leading to lower diversity libraries.
In the paper they state that PCR-free protocols offer obvious benefits in not introducing amplification biases or PCR errors that are impossible to distinguish from true SNVs. They also discuss how the emergence of greatly simplified protocols that merge library prep steps can significantly improve the workflow as well as the chemical efficiency of those merged steps. As a satisfied user of the Rubicon Genomics library prep technology (e.g. for ctDNA exomes) I'd like to have seen this included in the comparison*. In a 2014 post I listed almost 30 different providers.
Hidden ligation inefficiency: The analysis of ligation efficiency by the authors sheds light on an issue that has been discussed by many NGS users - that of whether library yield is an important QC or not? Essentially yield is a measure of how much library a kit can generate from a particular sample, but it is not a measure of how "good" that library is. Only analysis of final library diversity can really act as a sensible QC.
The authors saw that kits with high adapter ligation efficiency gave similar yields when compared to kits with low adapter ligation efficiency (fig 4 reproduced above). They determined that the most likely cause was that the relatively high amount of adapter-ligated DNA going into PCR inhibits the PCR amplification reaction leading to lower than expected yields. For libraries with low adapter ligation efficiency a much lower amount of adapter-ligated DNA would make it into PCR, but because there is no inhibition the PCR amplification reaction leads to higher than expected yields. The best performing kits were Illumina Truseq Nano and PCR free, and KAPA Hyper kit with ligation yields above 30%; and the KAPA HyperPlus was fully efficient.
Control amplicon bias: the PhiX control used had three separate PCR amplicons amplified to assess bias. The kits with the lowest bias at less than 25 % for each fragment size were KAPA HyperPlus and NEBNext. The Illumina TruSeq Nano kit showed different biases when using the "Sanger adaptors" rather than "Illumina adaptors", which the authors suggest highlights that both adapter and fragment sequence play a role in the cause of this bias.
Which kit to choose: The authors took the same decision as most kit comparison papers and shied away from making overt claims about which kit was "best". The did discuss fragmentation and PCR-free as important points to consider.
- If you have lots of DNA then aim for PCR-free to remove any amplification errors and/or bias.
- If you don't have a Covaris then newest enzymatic shearing methods e.g. KAPA fragmentase have significantly less bias than previous chemical fragmentation methods.
*Disclosure: I am a paid member of Rubicon Genomics' SAB.