The effect of genome graph expressiveness on the discrepancy between genome graph distance and string set distance.

ABSTRACT:

Motivation

Intra-sample heterogeneity describes the phenomenon where a genomic sample contains a diverse set of genomic sequences. In practice, the true string sets in a sample are often unknown due to limitations in sequencing technology. In order to compare heterogeneous samples, genome graphs can be used to represent such sets of strings. However, a genome graph is generally able to represent a string set universe that contains multiple sets of strings in addition to the true string set. This difference between genome graphs and string sets is not well characterized. As a result, a distance metric between genome graphs may not match the distance between true string sets.

Results

We extend a genome graph distance metric, Graph Traversal Edit Distance (GTED) proposed by Ebr

SUBMITTER: Qiu Y 

PROVIDER: S-EPMC9235494 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature