ViReMa

ViReMa maps recombinant viral nucleic acids in high-throughput sequencing data to detect and annotate viral recombination events underlying intrahost diversity and viral evolution.

Key Features:

• Recombination Event Detection: Detects a wide array of viral recombination events, including duplications, deletions, copy/snap-back recombination, intervirus or intersegment recombination, and insertions of host nucleic acids.
• Algorithmic Foundation: Builds upon the bowtie short-read aligner and employs a bootstrapping approach to capture and annotate recombinant species within viral populations.
• Error Density Function: Incorporates an "error density" function to enhance detection accuracy in longer reads from modern Illumina sequencing platforms and in complex mutational landscapes with multiple events.
• Standardized Output Reports: Produces standardized output reports for various recombinant species to facilitate interpretation and comparison across datasets.

Scientific Applications:

• Deletion Events: Reports deletion events in simulated data such as Flock House virus.
• Copy-back RNA Species: Identifies copy-back RNA species in Sendai viruses.
• Short Duplication Events: Detects short duplication events in HIV.
• Virus-to-Host Recombination: Identifies recombination events between viral and host nucleic acids as observed in an archaeal DNA virus.

Methodology:

Uses the bowtie short-read aligner with a bootstrapping approach and an error density function to detect and annotate recombinant viral species from high-throughput sequencing data.