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

By O. Dudchenko, Muhammad Saad Shamim, S. Batra, Neva C. Durand, Nathaniel T. Musial, Ragib Mostofa, Melanie Pham, Brian Glenn St Hilaire, Weijie Yao, Elena K. Stamenova and 11 more. bioRxiv, 2018

332 citations recorded by the source corpus.

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.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/b34950dd724f90060d97378e0306ff4d9c4b39b6

Citations in the corpus

• Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing (2022, unknown): “Finally, each set of scaffolds was manually validated and corrected with Juicebox Assembly Tools and the assemblies were packaged according to our Pan-Sol specification (https:// github. com/ pan-sol/ pan- sol-spec) [23].”