title: pigeon_pox in oesophagus:pigeon
design: Sequencing was performed using MinION (nanopore) sequencing technology and long reads were obtained. Basecalling and demultiplexing was perfomed using guppy basecaller and barcoder respectively. Quality control was assessed, and samples were trimmed using porechop before being mapped to the Pigeonpox virus isolate (FeP2) reference sequence, downloaded from NCBI (NC_024447.1:193678-195654), representing the region amplified by the PCR primers. Minimap2 was using for mapping and bcftools (mpileup), vcfutils.pl, and seqtk were used to map the fastq files and generate consensus sequences for the virus isolates. Alignment was performed using mafft and phylogenetic analysis using MEGA. A maximum likelihood tree was generated using 100 bootstraps and gamma distributed invariant sites.