A tri-tuple coordinate system derived for fast and accurate analysis of the colored de Bruijn graph-based pangenomes.

ABSTRACT:

Background

With the rapid development of accurate sequencing and assembly technologies, an increasing number of high-quality chromosome-level and haplotype-resolved assemblies of genomic sequences have been derived, from which there will be great opportunities for computational pangenomics. Although genome graphs are among the most useful models for pangenome representation, their structural complexity makes it difficult to present genome information intuitively, such as the linear reference genome. Thus, efficiently and accurately analyzing the genome graph spatial structure and coordinating the information remains a substantial challenge.

Results

We developed a new method, a colored superbubble (cSupB), that can overcome the complexity of graphs and organize a set of speci

SUBMITTER: Guo J 

PROVIDER: S-EPMC8161984 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature