Abstract
The cost and portability of the Oxford Nanopore Technologies MinION make it a good candidate for detection of food and waterborne parasites. As a step toward developing the MinION as a tool for detection of food and waterborne parasites, we have evaluated the accuracy of genome assemblies produced from MinION sequencing data on a food- and waterborne parasite – Giardia duodenalis. Two strains of G. duodenalis that have reference genomes available in the literature (G. duodenalis Assemblage A isolate WB and G. duodenalis Assemblage B isolate GS) were re-sequenced on the MinION. De novo genome assemblies were performed using combinations of 1D or 1Dsq reads produced by sequencing, pooling data from sequencing runs for the same organism, and using different long read assemblers (Canu, Abruijn, or SMARTdenovo). The resulting assemblies then underwent up to eight rounds of genome polishing. The 207 draft assemblies were then compared against the reference genomes and evaluated on their average percent identity, proportion of mismatching bases, number of insertions and deletions per 1000 aligned bases, average size of insertions and deletions, and proportion of the reference genome that they covered between zero-and-four times. The assemblies were also evaluated on their overall size, number of contigs, and the number of known genes each was found to contain. The optimal assembly pipeline for Giardia sequences generated on the MinION was found to be 1D reads assembled with SMARTdenovo followed by four or five rounds of genome polishing with the program Nanopolish.