Illumina reads of genomic DNA from bacteria isolated from uterus of dairy cows
For long-read sequencing, gDNA was extracted using the Monarch HMW DNA Extraction Kit following the protocol for high molecular weight DNA extraction from bacteria (NEB #T3060, New England Biolabs). Genomic DNA purity was measured using a NanoDrop 2000 spectrophotometer; final concentration was confirmed with a Qubit 2.0 Fluorometer (Thermo Scientific). The integrity of the extracted gDNA was evaluated via agarose gel electrophoresis to visually assess that the final product contained a large portion of DNA fragments longer than 20Kbp and little shearing. Nanopore sequencing samples were prepared using Oxford Nanopores Genomic DNA by Ligation kit and protocol. All samples were run on Nanopore R9 flow cells (R9.4.1) on a MinION. Post-sequencing, we used Guppy, version 5.0.16 in high-accuracy base calling mode.