MALVIRUS

MALVIRUS genotypes haploid viral genomes directly from sequencing data without assembly or reference mapping, producing SNP and indel calls and supporting Pango lineage assignment for virological analyses.

Key Features:

• Rapid Genotyping: Per-sample genotyping from sequencing reads can be completed within minutes.
• Variant Catalog Creation: Builds a population-level variant catalog including single nucleotide polymorphisms (SNPs) and insertions/deletions (indels).
• Efficient Genotype Calling: Uses the variant catalog to call and annotate genotypes from a read sample.
• Pango Lineage Assignment: Assigns SARS-CoV-2 input samples to most likely Pango lineages based on genotyped variations.
• Versatile Data Compatibility: Accepts and has been tested on Illumina and Nanopore sequencing data.
• Reusability: Reuses a pre-built variant catalog to genotype multiple individuals.

Scientific Applications:

• Viral population genotyping: Characterizes genetic variation within viral populations through SNP and indel calls.
• SARS-CoV-2 surveillance and lineage tracking: Supports assignment of samples to Pango lineages for monitoring variants during outbreaks.

Methodology:

Two computational steps are used: variant catalog creation from population sequences using mafft and snp-sites, and genotype calling using KMC and MALVA against the pre-built catalog.