Assembly of TSPV Genome
Initially, both viral DNA and viral RNA were extracted using the QIAamp Mini Elute Virus Spin Kit according to manufacturers instructions. DNA was then removed using a Turbo DNAse treatment. The True Seq mRNA library preparation kit was used before single-end sequencing, for 100 cycles, on an Illumina Hi-Seq 4000 (Institute of Biotechnology at Cornell University). For each dataset, adapters were removed using Trimmomatic and PhiX174 contaminants were removed using Bowtie 2 (--very-sensitive-local).