Figure 4: Extensive classification and coverage map.
From: VIP: an integrated pipeline for metagenomics of virus identification and discovery
All high quality reads were subject to viral database using nucleotide alignment (Bowtie2) or amino acid alignment (RAPSearch2). Reads would be classified into each viral genus based on alignment results. VIP would choose a close reference based on abundance of reference genome due to the proposed hypothesis that the genome coverage percentage was alongside with the genome sequencing depth. Candidate reads would map against to the selected reference with optimal BLASTn at reward/penalty score (1/−1), followed by coverage map generation.
