The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000 (original) (raw)

New Results

, View ORCID ProfileMuhammad S. Shamim, View ORCID ProfileSanjit S. Batra, Neva C. Durand, Nathaniel T. Musial, Ragib Mostofa, Melanie Pham, Brian Glenn St Hilaire, Weijie Yao, Elena Stamenova, Marie Hoeger, Sarah K. Nyquist, Valeriya Korchina, Kelcie Pletch, Joseph P. Flanagan, Ania Tomaszewicz, Denise McAloose, Cynthia Pérez Estrada, Ben J. Novak, View ORCID ProfileArina D. Omer, View ORCID ProfileErez Lieberman Aiden

doi: https://doi.org/10.1101/254797

Abstract

Hi-C contact maps are valuable for genome assembly (Lieberman-Aiden, van Berkum et al. 2009; Burton et al. 2013; Dudchenko et al. 2017). Recently, we developed Juicebox, a system for the visual exploration of Hi-C data (Durand, Robinson et al. 2016), and 3D-DNA, an automated pipeline for using Hi-C data to assemble genomes (Dudchenko et al. 2017). Here, we introduce “Assembly Tools,” a new module for Juicebox, which provides a point-and-click interface for using Hi-C heatmaps to identify and correct errors in a genome assembly. Together, 3D-DNA and the Juicebox Assembly Tools greatly reduce the cost of accurately assembling complex eukaryotic genomes. To illustrate, we generated de novo assemblies with chromosome-length scaffolds for three mammals: the wombat, Vombatus ursinus (3.3Gb), the Virginia opossum, Didelphis virginiana (3.3Gb), and the raccoon, Procyon lotor (2.5Gb). The only inputs for each assembly were Illumina reads from a short insert DNA-Seq library (300 million Illumina reads, maximum length 2x150 bases) and an in situ Hi-C library (100 million Illumina reads, maximum read length 2x150 bases), which cost <$1000.

The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.