Strainline

Strainline reconstructs full-length viral haplotypes de novo from noisy third-generation long-read sequencing data without requiring a reference genome.

Key Features:

• De Novo Assembly: Strainline performs de novo assembly to construct complete viral genomes without relying on a reference.
• Haplotype Resolution: Strainline preserves haplotype-specific variation to resolve individual viral haplotypes rather than producing a consensus sequence.
• No Reference Genome Required: Strainline operates without a reference genome, enabling analysis of novel or highly divergent viruses.
• Third-Generation Long-Read Support: Strainline leverages third-generation long-read sequencing data as its input.
• Algorithms for Noisy Data: Strainline employs algorithms tailored to handle the high error rates inherent to noisy long reads.
• Full-Length Haplotype Reconstruction: Strainline reconstructs full-length viral haplotypes with high accuracy and resolution.

Scientific Applications:

• Viral Diversity Studies: By resolving individual haplotypes, Strainline enables analysis of genetic variation within viral quasispecies to inform studies of evolution, transmission, and pathogenicity.
• Disease Management: Strainline's reconstruction of the full spectrum of viral diversity aids identification of conserved and variable regions relevant for vaccine and antiviral development.
• Outbreak Investigation: Strainline provides detailed genetic profiles from long-read data useful for genomic characterization during outbreak responses.

Methodology:

Strainline uses third-generation long-read sequencing data and algorithms specifically tailored to handle noisy reads to perform de novo assembly and reconstruct full-length viral haplotypes without a reference genome.