Synthetic environmental metagenomes for MinION evalutation

Environmental metagenomics is accomplished by annotation of WGS sequences or assignment of taxonomy based on 16S amplicon sequences. Both of these approaches provide species annotations that are limited by read length. A nanopore-based sequencing platform, MinION™, produces reads 1e+04 bp and greater, which has the potential to provide for more precise assignment of taxa, thereby alleviating some of the error inherent in determining metagenome composition from short reads. In this study, we tested the ability of sequence data produced by the MinION™ nanopore platform to correctly classify prokaryotes in single-species runs (R7.3 flow cells) and in two types of simple mixed synthetic communities: an equimolar mixture of DNA from four species (using R7.3 and Mk1 flow cells) and a community with one relatively rare (1%) component (both R7.3 and Mk1 flow cells). Community analysis was performed by three methods: BLAST, KRACKEN, and MG-RAST.