Veli Mäkinen

This paper introduces a seed-chain-extend alignment workflow using elastic founder graphs to improve sequence-to-graph alignment accuracy and efficiency in pangenomics.

GraphChainer improves alignment of erroneous long reads to acyclic variation graphs, aligning more reads and total read length than existing tools.

The paper introduces a pipeline for genomic epidemiology using mixed samples, showing comparable results to colony picks in a nosocomial setting.

uLTRA improves long-read RNA sequencing alignment accuracy using a two-pass collinear chaining algorithm, outperforming existing tools on simulated and biological data.

This paper generalizes sequence-to-sequence alignment algorithms to graphs, achieving significant speedups for aligning sequencing reads to variation graphs.

CHIC is a short-read aligner designed for pan-genomic references, using a hybrid compression and alignment approach to handle large and repetitive datasets.

BasePlayer is a software tool for analyzing large-scale NGS data, enabling variant analysis, visualization, and integration of genomic data.

The paper enhances variation detection by using pan-genome indexing to create a recombined reference sequence from multiple alignments, improving detection on real datasets.