Ultra-Low Coverage Sequencing as the Most Accurate Library Quantification Method Prior to Target Sequencing

Abstract

Accurate library quantification is very important during post-pooling captured target sequencing. There are a number of methods available to quantify libraries prior to sequencing, but no gold standard for the quantification of libraries exists. In this study, we compared common library quantification methods (Labchip, Qubit 3.0, qPCR with three primer sets) with ultra-low coverage sequencing (MiSeq with and without insert size correction). Cost, time and quantification accuracy were considered. We found that Qubit and MiSeq were better than qPCR and LabChip at predicting the final concentration. Also we revealed that MiSeq with insert size correction was the most accurate method for library quantification prior to target sequencing. This method allows for correction shifts in the ratio due to enrichment. Ultra-low coverage sequencing by Illumina MiSeq is the most accurate method for library quantification prior to pooling and post-pooling target enrichment.