NPGREAT: assembly of human subtelomere regions with the use of ultralong nanopore reads and linked-reads.

ABSTRACT:

Background

Human subtelomeric DNA regulates the length and stability of adjacent telomeres that are critical for cellular function, and contains many gene/pseudogene families. Large evolutionarily recent segmental duplications and associated structural variation in human subtelomeres has made complete sequencing and assembly of these regions difficult to impossible for many loci, complicating or precluding a wide range of genetic analyses to investigate their function.

Results

We present a hybrid assembly method, NanoPore Guided REgional Assembly Tool (NPGREAT), which combines Linked-Read data with mapped ultralong nanopore reads spanning subtelomeric segmental duplications to potentially overcome these difficulties. Linked-Read sets of DNA sequences identified by matches wi

SUBMITTER: Adam E 

PROVIDER: S-EPMC9758922 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature