Accurate determination of node and arc multiplicities in de bruijn graphs using conditional random fields.

ABSTRACT:

Background

De Bruijn graphs are key data structures for the analysis of next-generation sequencing data. They efficiently represent the overlap between reads and hence, also the underlying genome sequence. However, sequencing errors and repeated subsequences render the identification of the true underlying sequence difficult. A key step in this process is the inference of the multiplicities of nodes and arcs in the graph. These multiplicities correspond to the number of times each k-mer (resp. k+1-mer) implied by a node (resp. arc) is present in the genomic sequence. Determining multiplicities thus reveals the repeat structure and presence of sequencing errors. Multiplicities of nodes/arcs in the de Bruijn graph are reflected in their coverage, however, coverage variability and cov

SUBMITTER: Steyaert A 

PROVIDER: S-EPMC7491180 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature