Pseudomonas PF05 short reads
Raw reads were firstly filtered to discard contaminants from humans or bacterial species other than the targeted one, using different strategies. For human contamination, the generated reads were aligned against GRCh38 (hg38) human genome and filtered by alignment quality. MetaPhlAn 4.0 (1) and Kraken v2 (2) software were used to quantify bacterial species contamination. Next, the genome was assembled de novo using Unicycler (3) and contigs with low coverage were discarded. The quality of the assembly was assessed by the Quast software (v 5.2.0) (4). Functional annotations were performed using the BAKTA software (v. 1.7.0; database version 5.0) (5).