Lossless indexing with counting de Bruijn graphs.

ABSTRACT: Sequencing data are rapidly accumulating in public repositories. Making this resource accessible for interactive analysis at scale requires efficient approaches for its storage and indexing. There have recently been remarkable advances in building compressed representations of annotated (or colored) de Bruijn graphs for efficiently indexing k-mer sets. However, approaches for representing quantitative attributes such as gene expression or genome positions in a general manner have remained underexplored. In this work, we propose counting de Bruijn graphs, a notion generalizing annotated de Bruijn graphs by supplementing each node-label relation with one or many attributes (e.g., a k-mer count or its positions). Counting de Bruijn graphs index k</

SUBMITTER: Karasikov M 

PROVIDER: S-EPMC9528980 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature