title: WGS of Pseudomonas aeruginosa: hospital sink drain
design: Bacterial isolates were streaked on Blood Agar plates and grown at 37oC overnight. Single colonies were used to inoculate overnight liquid cultures in Kings Medium B and grown at 30oC with vigorous shaking. Genomic DNA was extracted from 700 ul of overnight culture using the Puregene Yeast and Bacteria kit (Qiagen, MD, USA). Illumina libraries with 300 to 400 bp insert size were generated using the Illumina Nextera XT kit according to the manufacturers protocol (Illumina, CA, USA). Libraries were dual-barcoded with the Nextera XT Index kit containing up to 384 indices (Illumina, CA, USA). Libraries were pooled in equal amounts and sequenced on the Illumina NextSeq 500 with 150 base PE reads. The Paired Reads have been trimmed with trimmomatic v0.36: trimmomatic PE -threads 40 \raw_reads/$i"_R1.fastq.gz" raw_reads/$i"_R2.fastq.gz" \trimmed_reads/$i"_R1.fastq.gz" \unpaired_reads/$i"_unpaired_R1.fastq.gz" \trimmed_reads/$i"_R2.fastq.gz" \unpaired_reads/$i"_unpaired_R2.fastq.gz" \CROP:150 SLIDINGWINDOW:4:5 \ILLUMINACLIP:NexteraPE-PE.fa:2:30:10 \MINLEN:100