Skip to content

Tool Selection Guide

This guide helps you choose the right tools for your virome analysis workflow based on your specific research questions and sample types.

Key Decision Factors

When selecting tools for virome analysis, consider these key factors:

  1. Research Objective - What is your primary research question?
  2. Sample Type - What environment does your sample come from?
  3. Computational Resources - What computing resources do you have available?
  4. Specific Requirements - Do you have special needs like sensitivity, runtime, or database dependencies?

Decision Flowchart

Tool Selection Start
↓
What is your primary objective?

Virus Detection

Identification Tools
↓
Sample type?
Metagenome:
VirSorter2
VIBRANT
geNomad
Transcriptome:
RNA-Virus-Flow
RdRp-scan
Single cell:
scVIRseq
scViroCap

Host Prediction

Host Prediction Tools
↓
Host domain?
Bacteria:
WIsH
iPHoP
PHIST
Eukaryotes:
DeepHost
VirHostMatcher-Net

Genome Analysis

Assembly:
metaviralSPAdes
metaPhage
Annotation:
Pharokka
DRAMv
Quality Check:
CheckV
viralComplete

Classification

Taxonomy:
vConTACT2
PhaGCN
VIPtree
Function:
BACPHLIP
PHROGs

Tool Selection by Category

Virus Identification

Tool Strengths Limitations Best For
VirSorter2 Sensitive, handles diverse viral sequences Computationally intensive Metagenomes with unknown viruses
VIBRANT Integrated annotation, good visualization Limited to specific viral groups Phage-focused studies
DeepVirFinder Works well on short contigs Requires GPU for best performance Fragmented assemblies
Seeker Ultra-fast, works on reads Lower accuracy than contig-based tools Quick screening

Host Prediction

Tool Strengths Limitations Best For
WIsH Fast, accurate for bacteria Requires reference genomes Phage-host studies
iPHoP Multi-method approach Computationally intensive When accuracy is critical
PHIST Simple k-mer based May miss distant relationships Quick screening
VirHostMatcher-Net Works across domains Requires training Cross-domain studies

Genome Assembly

Tool Strengths Limitations Best For
metaviralSPAdes Specifically for viral metagenomes Memory intensive Complex viral communities
metaPhage Optimized for phages Limited to phages Bacteriophage studies
PHAMB Good for retrieving viral contigs Requires good depth Well-sequenced samples

Computational Requirements

Resource Level Recommended Tools
Low (Laptop) Seeker, PHIST, VirHostMatcher
Medium (Workstation) VirSorter2, VIBRANT, WIsH
High (Server/Cluster) metaviralSPAdes, iPHoP, PHAMB
Cloud-optimized IDseq, CZ ID, Jovian

Recent Additions (2024-2025)

These tools have been added recently and show promising results:

  • DePhT - Novel approach to detect prophages with high accuracy
  • GraViTy - Graph-based virus taxonomy assignment tool
  • ViroProfiler - Integrated workflow for comprehensive virome profiling
  • ViralWasm - Web Assembly tools for client-side viral analysis
  • CHERRY - AI-based identification and classification of animal viruses

Version Compatibility

Tool Python Version Dependencies
VirSorter2 3.6+ scikit-learn, Tensorflow
VIBRANT 3.5+ scikit-learn, prodigal
iPHoP 3.7+ mash, pytorch, diamond
MetaviralSPAdes Any C++17 compiler
Pharokka 3.8+ BLAST+, mash, prodigal

Further Resources