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

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.
Subject Area
- Biochemistry (7342)
- Bioengineering (5318)
- Bioinformatics (20249)
- Biophysics (10002)
- Cancer Biology (7735)
- Cell Biology (11292)
- Clinical Trials (138)
- Developmental Biology (6431)
- Ecology (9943)
- Epidemiology (2065)
- Evolutionary Biology (13312)
- Genetics (9358)
- Genomics (12577)
- Immunology (7696)
- Microbiology (19000)
- Molecular Biology (7433)
- Neuroscience (40976)
- Paleontology (300)
- Pathology (1228)
- Pharmacology and Toxicology (2133)
- Physiology (3155)
- Plant Biology (6857)
- Synthetic Biology (1895)
- Systems Biology (5310)
- Zoology (1087)