mixed DNa and RNA seq of pigeon: cloaca swab
The transport medium for viruses was purified using 0.8 m polyethersulphone spin filters to enrich for viral particles before nuclease treatment and nucleic acid extraction. Further DNA/RNA enrichment and library preparation was done. Then, third-generation sequencing was performed. The acquired raw data were converted to bases using Guppy v 7.1.4, quality filtered and taxonomically classified using in-house bioinformatics pipelines at PathoSense (Belgium). Then, the viral genome sequences were de novo assembled using Canu v2.2 and Medaka v1.11.1 tools.