fastv

fastv detects microbial sequences and types viruses and microorganisms by applying k-mer-based mapping and extension to sequencing data for rapid identification from short-read (Illumina, BGI) and long-read (ONT, PacBio) platforms.

Key Features:

• K-mer mapping and extension: fastv uses k-mer mapping and extension to rapidly detect microbial sequences in sequencing data.
• UniqueKMER integration: Includes UniqueKMER to generate complete sets of unique k-mers per genome and provides pre-generated unique k-mer sets for numerous human-affecting microorganisms and common viruses.
• Pre-processing: Automatically performs adapter trimming, quality pruning, and base correction prior to k-mer analysis.
• Sequencing platform support: Supports short-read sequencing (Illumina, BGI) and long-read sequencing (ONT, PacBio).
• Output and visualization: Produces microbial genome coverage visualization and outputs results in HTML and JSON formats.
• SARS-CoV-2 identification and typing: Provides built-in SARS-CoV-2 identification and typing with reported 100% sensitivity and specificity in experimental validation distinguishing it from SARS and MERS.

Scientific Applications:

• Rapid microbial identification: Rapid detection and characterization of viruses and microorganisms from sequencing data.
• Viral outbreak investigations: Application in investigations of viral outbreaks using sequencing-derived detections.
• Pathogen surveillance: Use in surveillance programs to monitor presence and types of pathogens.
• Microbiome analyses: Application to microbiome studies using both short-read and long-read sequencing data.
• SARS-CoV-2 monitoring and typing: Use in COVID-19 monitoring and typing workflows leveraging high reported sensitivity and specificity.

Methodology:

fastv applies adapter trimming, quality pruning, and base correction, then performs k-mer mapping and extension using UniqueKMER-generated unique k-mers for microbial identification.