Features

Sample Management

Management
  • Track samples from creation to analysis.
  • Quickly and easily search and filter sample records.
Creation
  • Create sample records from paired and unpaired FASTQ files
  • Error correction, trimming, and quality assessment is performed automatically.
QA
  • View sample quality metrics generated during import in clean, readable graphics
  • Analysis and graphics based on FastQC, the most commonly used next-gen QC tool.
  • Export quality graphics to PDF.

Analysis

Detect Known Viruses
  • Quickly assess sample libraries for the presence of viruses in Virtool's reference database.
  • Based on tools such as Bowtie2 and Pathoscope.
Discover Novel Viruses
  • Use our novel analytical pipeline, NuVs, to find previously unknown viruses.
  • Uses SPAdes and HMMER.
  • Inspired by vFAM.

References

Multiple References
  • Maintain multiple reference sets for different classes of pathogens or pests.
Manage OTUs
  • Easily browse and edit the organizational taxonomic units (OTUs) in a reference.
Structured OTUs
  • Easily create and edit OTUs without editing files
  • Track and detect multiple isolates or strains of an OTU
  • Enter multiple sequence segments and automatically retrieve data based on Genbank accessions
History
  • Track every change ever made to an OTU
  • Easily revert uncommitted changes
Versioning
  • Follow a natural versioning lifecycle by building optimized mapping indexes when valid changes have been made to the reference

Subtractions

Create Subtractions
  • Create subtraction indexes for removing unwanted sequencing data from analyses

Job Management

Tracking
  • Manage and track resource-intensive tasks such as analyses or sample creation.
Staging
  • Find out where indiviual jobs are in there lifecycles

User Management

Manage Users
  • Add or remove users and control their access and permissions.
Control Activity Using Groups
  • Assign group ownership and rights to samples
  • Control reference access and modification rights by user and group
  • Restrict activity using group permissions

Software Updates

Easily Track and Install Software Updates

Easily Track and Install Software Updates
  • Automatically track software updates for Virtool
  • Install updates from within the web interface