Characterizing tandem repeat complexities across long-read sequencing platforms with TREAT and <i>otter</i>.

ABSTRACT: Tandem repeats (TRs) play important roles in genomic variation and disease risk in humans. Long-read sequencing allows for the accurate characterization of TRs; however, the underlying bioinformatics perspectives remain challenging. We present otter and TREAT: otter is a fast targeted local assembler, cross-compatible across different sequencing platforms. It is integrated in TREAT, an end-to-end workflow for TR characterization, visualization, and analysis across multiple genomes. In a comparison with existing tools based on long-read sequencing data from both Oxford Nanopore Technology (ONT, Simplex and Duplex) and Pacific Bioscience (PacBio, Sequel II and Revio), otter and TREAT achieve state-of-the-art genotyping and motif characterization accuracy. Applied to clin

SUBMITTER: Tesi N 

PROVIDER: S-EPMC11610572 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature