Illumina NextSeq 500 WGS of Mannheimia haemolytica: bovine, deep nasopharyngeal swab
DNA was extracted from 24 hour cultures of the selected isolates grown on blood agar plates at 37 C, using a commercially available kit (Ultraclean Microbial DNA Isolation Kit, Qiagen, Germantown, MD), and assessed for purity and concentration with a NanoDrop spectrophotometer (ThermoFisher Scientific, Waltham, MA); all samples had A260/A280  values > 1.80. Extracted DNA was submitted to the Georgia Genomics and Bioinformatics Core  for sequencing. Sequence libraries were synthesized with a Kapa Hyper Prep Kit (Kapa Biosystems, Wilmington, MA) and sequencing was performed on an Illumina NextSeq 500 instrument (Illumina Inc., San Diego, CA). Sequence data was quality trimmed, assembled and annotated by the UGA Georgia Genomics and Bioinformatics Core. FastQC, version 0.11.5, was used to assess quality metrics for both raw and trimmed reads. Quality trimming and filtering of reads was performed using Trimmomatic, version 0.36, with only paired-end reads ? 50 bases maintained for downstream assembly. The average number of reads per sample for the raw and trimmed reads was 7.3 million and 6.5 million, respectively. The percentage of paired reads remaining after trimming ranged from a low of 80% to a high of 91%. The total number of trimmed, paired reads ranged from a low of 3.9 million to a high of 9.7 million.