DENTIST-using long reads for closing assembly gaps at high accuracy.

ABSTRACT:

Background

Long sequencing reads allow increasing contiguity and completeness of fragmented, short-read-based genome assemblies by closing assembly gaps, ideally at high accuracy. While several gap-closing methods have been developed, these methods often close an assembly gap with sequence that does not accurately represent the true sequence.

Findings

Here, we present DENTIST, a sensitive, highly accurate, and automated pipeline method to close gaps in short-read assemblies with long error-prone reads. DENTIST comprehensively determines repetitive assembly regions to identify reliable and unambiguous alignments of long reads to the correct loci, integrates a consensus sequence computation step to obtain a high base accuracy for the inserted sequence, and validates the accura

SUBMITTER: Ludwig A 

PROVIDER: S-EPMC8848313 | biostudies-literature | 2022 Jan

REPOSITORIES: biostudies-literature