Fredrik O. Vannberg

Using Earth Mover’s Distance for Viral Outbreak Investigations

This paper introduces a method using k-mer distribution in RNA-seq reads to estimate genetic relatedness between viral samples and infer transmission clusters without requiring full RNA-seq assembly.

Next-generation Sequence-analysis Toolkit (NeST): A standardized bioinformatics framework for analyzing Single Nucleotide Polymorphisms in next-generation sequencing data

NeST is a variant calling framework that combines multiple callers to improve accuracy in identifying SNPs from NGS data, validated on Plasmodium falciparum isolates.

Mapping-free variant calling using haplotype reconstruction from k-mer frequencies

The paper introduces Kestrel, a k-mer-based variant caller that avoids mapping, assembly, and de Bruijn graphs, achieving high concordance with assembled contigs in Streptococcus pneumoniae.