Solving scaffolding problem with repeats

Mandric, I.; Zelikovsky, A.

doi:10.1101/330472

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bioRxiv · 10.1101/330472

Solving scaffolding problem with repeats

Mandric, I.·Zelikovsky, A.

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Abstract

One of the most important steps in genome assembly is scaffolding. Increasing the length of sequencing reads allows assembling short genomes but assembly of long repeat-rich genomes remains one of the most interesting and challenging problems in bioinformatics. There is a high demand in developing computational approaches for repeat aware scaffolding. In this paper, we propose a novel repeat-aware scaffolder BATISCAF based on the optimization formulation for filtering out repeated and short contigs. Our experiments with five benchmarking datasets show that the proposed tool BATISCAF outperforms state-of-the-art tools. BATISCAF is freely available on GitHub: https://github.com/mandricigor/batiscaf.

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Mandric, I., Zelikovsky, A.. 2018-05-25. Solving scaffolding problem with repeats. https://doi.org/10.1101/330472

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