NGS of bluetongue virus from a sheeppox vaccine
A pre-alignment quality check was performed using the FASTQC program and the Trim Galore script was used for quality and adapter trimming of FASTQ files along with removal of short sequences (<50bp). Subsequently, reads were mapped to a range of reference sequences using the BWA-MEM tool and then the DiversiTools software was used to generate the consensus sequence. If the consensus sequence contained any gaps, a BLAST search was performed in order to find a more suitable reference sequence. Finally, the consensus sequence was used as a reference sequence to increase the number of BTV reads mapped to the reference, and the final consensus sequence was saved and used for further analysis.