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

By Jay Ghurye, Arang Rhie, Brian P. Walenz, Anthony Schmitt, Siddarth Selvaraj, Mihai Pop, Adam M Phillippy, Sergey Koren

Posted 07 Feb 2018
bioRxiv DOI: 10.1101/261149 (published DOI: 10.1371/journal.pcbi.1007273)

Motivation: 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. Results: 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. Availability and Implementation: The Python and C++ code for our method is openly available at https://github.com/machinegun/SALSA.

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