Scalable variant detection in pangenome models @T2T-HPRC 2020 Conference

PANGAIA > News&Events > News > Scalable variant detection in pangenome models @T2T-HPRC 2020 Conference

Congratulations to Porto et al. for their poster at the T2T HPRC conference.

Abstract

We have implemented a two-step scalable approach to detect variants: first we construct a graph pangenome from a graphical fragment assembly (GFA) file that stores the fragments, where each fragment corresponds to a vertex of the graph, then we analyze the graph to detect all variants. We have tested our approach on a SARS-CoV-2 dataset with over 7800 fragments and on a dataset that contains all alternative sequences of the highly polymorphic human leukocyte antigen (HLA) complex.

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