Nanopore WGS of urinary pathogen E. coli R60
Genomic DNA from E. coli isolate 60 was extracted by phenolchloroform, prepared with the Q20+ ligation kit SQK-LSK114, and sequenced on an Oxford Nanopore MinION (R10.4.1 flow-cell) to ~60 depth. Reads 1 kb were filtered with Filtlong and assembled in a Trycycler consensus workflow, then polished with Medaka (model r1041_e82_400bps_hac_v4.2.0) and Illumina-read Polypolish.