Figure 1: A schematic overview of the VIP pipeline.
From: VIP: an integrated pipeline for metagenomics of virus identification and discovery
Raw NGS reads are first preprocessed by removal of adapter, low-quality, and low-complexity sequences, followed by computational subtraction of host-related reads using Bowtie2. In fast mode, viruses are identified by Bowtie2 alignment to ViPR/IRD nucleotide DB. In sense mode, bacteria and related rRNA (ribosomal RNA) reads are removed and the remaining reads are aligned to virus database. Unmatched reads are then aligned to a viral protein database from NCBI Refseq DB using RAPSearch. All matched reads are classified under a genus for de novo assembly and phylogenetic analysis. VIP reports include reads distribution, a summary table of classified reads with taxonomic assignments. In addition, results of phylogenetic analysis and genomic coverage map are attached.
