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bioRxiv · 10.1101/261149

Integrating Hi-C links with assembly graphs for chromosome-scale assembly

Ghurye, J.·Rhie, A.·Walenz, B. P.·Schmitt, A.·Selvaraj, S.·Pop, M.·Phillippy, A. M.·Koren, S.
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Abstract

Long-read sequencing and novel long-range assays have revolutionized de novo genome assembly by automating the reconstruction of reference-quality genomes. In particular, Hi-C sequencing is becoming an economical method for generating chromosome-scale scaffolds. Despite its increasing popularity, there are limited open-source tools available. Errors, particularly inversions and fusions across chromosomes, remain higher than alternate scaffolding technologies. We present a novel open-source Hi-C scaffolder that does not require an a priori estimate of chromosome number and minimizes errors by scaffolding with the assistance of an assembly graph. We demonstrate higher accuracy than the state-of-the-art methods across a variety of Hi-C library preparations and input assembly sizes. The Python and C++ code for our method is openly available at https://github.com/machinegun/SALSA\n\nAuthor summaryHi-C technology was originally proposed to study the 3D organization of a genome. Recently, it has also been applied to assemble large eukaryotic genomes into chromosome-scale scaffolds. Despite this, there are few open source methods to generate these assemblies. Existing methods are also prone to small inversion errors due to noise in the Hi-C data. In this work, we address these challenges and develop a method, named SALSA2. SALSA2 uses sequence overlap information from an assembly graph to correct inversion errors and provide accurate chromosome-scale assemblies.

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Ghurye, J., Rhie, A., Walenz, B. P., Schmitt, A., Selvaraj, S., Pop, M., Phillippy, A. M., Koren, S.. 2018-02-07. Integrating Hi-C links with assembly graphs for chromosome-scale assembly. https://doi.org/10.1101/261149

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