Finding low-complexity DNA sequences with longdust

Abstract

Motivation: Low-complexity (LC) DNA sequences are compositionally repetitive sequences that are often associated with spurious homologous matches and variant calling artifacts. While algorithms for identifying LC sequences exist, they either do not define complexity mathematically or are inefficient with long or variable context windows. Results: Longdust is a new algorithm that efficiently identifies long LC sequences including centromeric satellite and tandem repeats with moderately long motifs. It defines string complexity by statistically modeling the k-mer count distribution with the parameters: the k-mer length, the context window size and a threshold on complexity. Longdust exhibits high performance on real data and high consistency with existing methods. Availability and implementation: https://github.com/lh3/longdust