Phytest

Phytest performs automated quality control checks on sequences, phylogenetic trees, and associated metadata to ensure data integrity in phylogenetic analyses, including applications during the SARS-CoV-2 pandemic.

Key Features:

• Automation of quality control checks: Automates checks on sequences, phylogenetic trees, and metadata to identify potential issues within datasets.
• Integration into pipelines: Integrates with existing phylogenetic analysis pipelines to apply quality control within workflows and real-time analyses.
• Real-world application: Has been applied in real-world scenarios, including use during the SARS-CoV-2 pandemic, to support quality assurance in timely analyses.

Scientific Applications:

• Evolutionary biology: Ensures quality of sequence and tree data used for phylogenetic inference in evolutionary studies.
• Epidemiology: Supports genomic epidemiology by validating data used for outbreak reconstruction and transmission analyses.
• Virology: Applies to viral genomic analyses, including SARS-CoV-2, to maintain integrity of sequence and phylogenetic data.
• Real-time analysis: Enables quality control within real-time pipelines to support timely, reliable phylogenetic results.

Methodology:

Conducts a series of automated checks on input sequences, phylogenetic trees, and metadata and integrates these quality control measures into real-time pipelines to detect inconsistencies or errors.