Shotgun WGS of chicken tracheal swab sample
Tracheal swabs were obtained from 4.5 week old commercial broilers exhibiting mild clinical signs of respiratory distress. Genomic DNA was extracted directly from a clinical sample by using a commercially available DNA isolation kit. Total 1ng of DNA was used to prepare library using Nextera XT Fragment Library Kit (Illumina). The 500 cycle MiSeq Reagent Kit v2 (Illumina, USA) was used and the whole-genome sequencing was performed using the Illumina MiSeq platform.