Detecting transposable elements in long-read genomes using sTELLeR.

ABSTRACT:

Motivation

Repeat elements, such as transposable elements (TE), are highly repetitive DNA sequences that compose around 50% of the genome. TEs such as Alu, SVA, HERV, and L1 elements can cause disease through disrupting genes, causing frameshift mutations or altering splicing patters. These are elements challenging to characterize using short-read genome sequencing, due to its read length and TEs repetitive nature. Long-read genome sequencing (lrGS) enables bridging of TEs, allowing increased resolution across repetitive DNA sequences. lrGS therefore present an opportunity for improved TE detection and analysis not only from a research perspective but also for future clinical detection. When choosing an lrGS TE caller, parameters such as runtime, CPU hours, sensitivity, precision,

SUBMITTER: Bilgrav Saether K 

PROVIDER: S-EPMC11601167 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature