Next Generation Sequencing of yellow fever virus: FNV-FC
Viral RNA was extracted from the undiluted virus stocks utilizing the Qiagen Viral RNA Mini Kit according to the manufacturers instructions. cDNA libraries were prepared with random hexamer priming and sequenced on the Illumina NextSeq 550 instrument for paired-end 75bp reads. The raw reads were trimmed using Trimmomatic (v 0.39) with a cutoff set a Q30. Reads shorter than 35 bases were discarded. The reads were aligned to published genomes of Asibi, 17D-204, FVV, and FNV viruses, and were aligned using Bowtie2 software with paired-end, very sensitive local parameters. Picardtools MarkDuplicates was used to remove PCR duplicates (Picardtools, Broad Institute, MIT).