Whole genome sequencing and denovo assembly of CMV from cassava infected plants
The DNA sequencing library for Oxford Nanopore sequencing was prepared using the Rapid Barcoding kit (SQK-RBK004) with 9.4.1 flow cells (Oxford Nanopore Technologies), according to the manufacturers instructions. All libraries were loaded directly onto the MinION that was connected to MinIT, and live base calling was enabled. The raw electrical signal from nanopore sequencing was based on the ONT Albacore Sequencing Pipeline to obtain raw fastq nucleotide sequences that were demultiplexed using Porechop (https://github.com/rrwick/Porechop). BLASTn searches against a custom CMV database were performed to identify CMV reads, which were assembled de novo in Geneious Prime to produce viral contigs. The novelty of CMV contigs was assessed using BLASTn searches against the NCBI database.