BWA-MEM alignment to Scutavirus chelonidalpha5 genome
All samples were stored at 20 C prior to DNA extraction. For blood samples, DNA was extracted using the QIAGEN Blood and Cell Culture DNA Kit (QIAGEN, Germany) and the Genomic-tip procedure (QIAGEN, Germany). For muscle and liver tissues, DNA was extracted using the QIAGEN Puregene Tissue Kit (QIAGEN, Germany) following the manufacturers protocols. DNA quantity and purity were assessed using a NanoDrop spectrophotometer (Thermo Fisher Scientific, USA) and Qubit fluorometer (Invitrogen, USA), respectively. DNA integrity was verified by agarose gel electrophoresis prior to sequencing. The genomic DNA samples were used to construct Illumina TruSeq Nano (150 bp paired-end) libraries that were sequenced on the Illumina HiSeq X platform (Illumina, USA),  targeting approximately 30x genome coverage.