FVE-novel

FVE-novel reconstructs complete or near-complete viral draft genomes from metagenomic datasets by mapping reads and iteratively assembling mapped reads to recover intact virus and phage genomes from fragmented contigs.

Key Features:

• Efficient Mapping: Uses FastViromeExplorer to map metagenomic reads against viral reference genomes or existing contigs.
• De novo Assembly and Scaffold Generation: Performs de novo assembly of mapped reads to produce initial scaffolds.
• Iterative Assembly Extension: Employs an iterative approach to extend initial scaffolds and bridge gaps between fragmented contigs.
• Hybrid Mapping-and-Assembly Strategy: Combines reference-based mapping with de novo assembly techniques to leverage strengths of both methods.

Scientific Applications:

• Oceanic metagenomic analysis: Applied to oceanic metagenomic samples to generate 268 viral scaffolds, with manual examination of the ten longest scaffolds yielding four complete viral genomes, two of which had no matches in existing databases and two related to known phages.

Methodology:

Reference-based mapping using FastViromeExplorer against viral reference genomes or existing contigs; de novo assembly of mapped reads to create initial scaffolds; iterative assembly extension to refine and extend scaffolds into final viral scaffolds, implemented as a hybrid mapping-plus-assembly approach.