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Article

Characterizing tandem repeat complexities across long-read sequencing platforms with TREAT and otter.

Genome research - 20 Nov 2024

Tesi Niccoló, Salazar Alex, Zhang Yaran, van der Lee Sven, Hulsman Marc, Knoop Lydian, Wijesekera Sanduni, Krizova Jana, Schneider Anne-Fleur, Pennings Maartje, Sleegers Kristel, Kamsteeg Erik-Jan, Reinders Marcel, Holstege Henne

Abstract excerpt

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...

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Identifiers

PMID: 39406499
DOI: 10.1101/gr.279351.124
PMCID: PMC11610572

Genes

ABCA7
APOC1
RFC1
SPI1

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