TY - JOUR T1 - Comparison of bacterial genome assembly software for MinION data JF - bioRxiv DO - 10.1101/049213 SP - 049213 AU - Kim Judge AU - Martin Hunt AU - Sandra Reuter AU - Alan Tracey AU - Michael A. Quail AU - Julian Parkhill AU - Sharon J. Peacock Y1 - 2016/01/01 UR - http://biorxiv.org/content/early/2016/05/24/049213.abstract N2 - Antimicrobial resistance genes can be carried on plasmids or on mobile elements integrated into the chromosome. We sequenced a multidrug resistant Enterobacter kobei genome isolated from wastewater in the United Kingdom, but were unable to conclusively identify plasmids from the short read assembly. Our aim was to compare and contrast the accuracy and characteristics of open source software (PBcR, Canu, miniasm and SPAdes) for the assembly of bacterial genomes (including plasmids) generated by the MinION instrument. Miniasm produced an assembly in the shortest time, but Canu produced the most accurate assembly overall. We found that MinION data alone was able to generate a contiguous and accurate assembly of an isolate with multiple plasmids. ER -