ULTR-asm: assembly of ultra long tandem repeat

Repetitive sequences are prevalent across all domains of life and play intricate roles in genetic regulation, stability, and evolution. To better understand the functions of these repetitive sequences, various methods have been developed for assembling short tandem repeats such as microsatellites, minisatellites, and satellites. However, existing assembly methods overlook a special case of ultra-long tandem repeat, where the length of a single repeat unit exceeds tens of thousands of base pairs. It is challenging for existing assembly methods to accurately reconstruct these repeatsHere we present ULTR-asm, an assembler specifically designed to tackle ultra-long tandem repeats. ULTR-asm builds on the overlap-layout-consensus (OLC) paradigm, with an additional polishing optimization step. Evaluations on simulated data demonstrated that ULTR-asm outperforms state-of-the-art assemblers, enhancing genome integrity and accuracy, and contributing to the assembly of more complete genomes.