Efficient short read mapping to a pangenome that is represented by a graph of ED strings.

ABSTRACT:

Motivation

A pangenome represents many diverse genome sequences of the same species. In order to cope with small variations as well as structural variations, recent research focused on the development of graph based models of pangenomes. Mapping is the process of finding the original location of a DNA read in a reference sequence, typically a genome. Using a pangenome instead of a (linear) reference genome can e.g. reduce mapping bias, the tendency to incorrectly map sequences that differ from the reference genome. Mapping reads to a graph, however, is more complex and needs more resources than mapping to a reference genome. Reducing the complexity of the graph by encoding simple variations like SNPs in a simple way can accelerate read mapping and reduce the memory requirements at

SUBMITTER: Buchler T 

PROVIDER: S-EPMC10232250 | biostudies-literature | 2023 May

REPOSITORIES: biostudies-literature