RT Journal Article
SR Electronic
T1 Comparison of bacterial genome assembly software for MinION data
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 049213
DO 10.1101/049213
A1 Kim Judge
A1 Martin Hunt
A1 Sandra Reuter
A1 Alan Tracey
A1 Michael A. Quail
A1 Julian Parkhill
A1 Sharon J. Peacock
YR 2016
UL http://biorxiv.org/content/early/2016/05/24/049213.abstract
AB 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.