279. The long and short of Nanopore genomic prediction: the effect of read length on prediction accuracy

Abstract

On-farm genomic selection using Oxford Nanopore Technologies’ portable DNA sequencer is a potential method to accelerate genetic gain in extensive agricultural enterprises. Oxford Nanopore sequencing provides a number of potential benefits including no theoretical read length limit. Here we investigate the effect of read length on the accuracy of genomic prediction from Oxford Nanopore data by creating a range of different read length distributions with average read lengths ranging between 2,569 bp and 110 bp. Read length was found to have limited effect on the accuracy of genomic prediction for the tested range. However, average read lengths below 500 bp demonstrated a significant increase in unmapped reads and reduced sequencing coverage. Importantly, this means to maximise data recovery from Nanopore flowcells, on-farm DNA libraries should have average read lengths greater than 500 bp. This finding will inform the requirements of the on-farm molecular sample preparation, such as DNA extraction and library preparation.