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Analysis Presets

ViroConstrictor includes a preset system (available since version 1.2.0) that provides optimized analysis settings for specific pathogens.

What Are Presets?

Presets are predefined analysis configurations tailored to specific viral families or pathogens. Different viruses require different analysis approaches - for example, segmented viruses like Influenza need different settings than non-segmented viruses like SARS-CoV-2.

How Presets Work

Automatic Selection

  • Input matching: ViroConstrictor matches your viral target name to the closest preset
  • Fuzzy matching: Exact matches aren't required - the system finds the best fit
  • Confidence threshold: Matches below 40% confidence use DEFAULT settings
  • Fallback: Unknown targets automatically use DEFAULT preset

Usage Options

  • Command-line: Use --target or --preset flag for entire analysis
  • Samplesheet: Specify individual presets via the "Virus" column
  • Disable: Use --disable-presets / -dp to force DEFAULT settings

When to Disable Presets

Use --disable-presets / -dp to force DEFAULT settings when:

  • Analyzing experimental or in-development sequencing protocols
  • Working with pathogens not covered by existing presets
  • Troubleshooting analysis issues
  • Requiring consistent settings across diverse viral targets

Available Presets

Version-Dependent Presets

Preset availability and settings may change between ViroConstrictor versions. The information below corresponds to the current documentation version shown at the top of this page.

Preset Matching Examples

ViroConstrictor uses fuzzy matching, so exact names aren't required:

  • --target influenza_a_h3n2 → matches INFLUENZA preset via INFLUENZA_A alias.
  • --target sars-cov-2 → matches SARSCOV2 preset via SARS-COV-2 alias.
  • --target measles_outbreak → matches PARAMYXOVIRIDAE preset via MEASLES alias.

Preset Details

Preset Preset Aliases for matching Optimizations
DEFAULT N/A Standard ViroConstrictor settings for general viral analysis.
Used when no specific preset matches or when presets are disabled.
SARSCOV2 SARS-COV-2, SARS2, COVID, COV, SARSCOV, CORONAVIRUS Optimized read-alignment settings for SARS-CoV-2 reference mapping.
Tailored for SARS coronavirus 2 genome analysis.
INFLUENZA FLU, INF, INFLU, INFLUENZA, INFLUENZA_A, INFLUENZA_B Enhanced read-filtering and alignment-filtering for segmented Influenza genomes.
Built-in compatibility for MBTuni-12/13 universal influenza primer amplicons.1
PARAMYXOVIRIDAE MEASLES, MUMPS, MEV, MUV, MEASLES_VIRUS, MUMPS_VIRUS, PARAMYXOVIRUS, PARAMYXOVIRIDAE, MORBILLIVIRUS, RUBULAVIRINAE, ORTHORUBULAVIRUS Specialized alignment-filtering for Paramyxoviridae family viruses with optimized settings to cover the non-coding region between Matrix and Fusion genes.
Covers Measles, Mumps, and related viruses.
HEPATOVIRUS HEPATOVIRUS, HEPATITIS_A, HEPATITIS_A_VIRUS, HAV Alignment-filtering optimized for Hepatovirus A. Includes specialized alignment-filtering settings for improved genome recovery to compensate for sequencing artefacts may result in Picornaviridae sequencing data.
Currently only tailored for Hepatovirus A.

Important Considerations

Matching Warnings

ViroConstrictor displays warnings when: - Low confidence matches: Your input has <40% similarity to any preset - Unexpected matches: Your target matches a potentially unintended preset - No match found: Your input doesn't match any preset sufficiently

Best Practices

  • Run with --dryrun first to verify preset assignments
  • Check warnings carefully after analysis completion
  • Use --disable-presets if matching seems incorrect

Requesting New Presets

Need a preset for a pathogen not currently supported? Submit a feature request on our GitHub with details about:

  • Target pathogen or viral family
  • Sequencing protocol used
  • Specific analysis challenges
  • Expected benefits from a custom preset

  1. Zhou B, Donnelly ME, Scholes DT, et al. Single-Reaction Genomic Amplification Accelerates Sequencing and Vaccine Production for Classical and Swine Origin Human Influenza A Viruses. Journal of Virology. 83, 10309-10313. ↩