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

Olga DudchenkoiD, Muhammad S. ShamimiD, Sanjit Singh BatraiD, Neva C. DurandiD, Nathaniel T. Musial, Ragib Mostofa, Melanie PhamiD, Brian Glenn St Hilaire, Weijie Yao, Elena K. Stamenova, Marie HoegeriD, Sarah K. NyquistiD, Valeriya Korchina, Kelcie Pletch, Joseph P. Flanagan, Ania Tomaszewicz, Denise McAlooseiD, Cynthia Pérez EstradaiD, Ben J. NovakiD, Arina D. OmeriD, Erez Lieberman AideniD

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Structured summary available · Jump to summary ↓

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.

Abstract summary

Claude Opus 5.5 · xhigh effort · 17 Oct 2026 · from the abstract · CC BY-NC 4.0

Point-and-click correction of misassemblies on Hi-C heatmaps, paired with the automated 3D-DNA pipeline, gave chromosome-length wombat, opossum and raccoon scaffolds from just short-insert DNA-Seq and in situ Hi-C reads.

Hi-C contact maps are useful for genome assembly, and the authors' earlier tools covered Hi-C visualization (Juicebox) and automated Hi-C scaffolding (3D-DNA). The new module adds interactive, visual error correction, and the authors argue the combination makes accurate assembly of complex eukaryotic genomes far cheaper.

Key results

  1. SuggestedThe 3D-DNA plus Assembly Tools workflow produced de novo assemblies with chromosome-length scaffolds for three mammals with multi-gigabase genomes.

    Wombat (Vombatus ursinus, 3.3Gb), Virginia opossum (Didelphis virginiana, 3.3Gb) and raccoon (Procyon lotor, 2.5Gb); the abstract gives no contiguity, completeness or accuracy statistics for these assemblies. · Abstract

  2. SuggestedEach assembly was built from standard short-read inputs only, at a stated cost below $1000 per genome.

    Per genome: 300 million reads from a short-insert DNA-Seq library and 100 million reads from an in situ Hi-C library, all Illumina with read lengths of at most 2x150 bases, together stated to cost <$1000; no cost breakdown is given in this text. · Abstract

  3. ClaimedThe authors present 3D-DNA combined with the Assembly Tools module as a way to substantially lower the cost of accurately assembling complex eukaryotic genomes.

    General statement in the abstract, illustrated only by the three mammalian assemblies; no head-to-head cost or quality comparison with other assembly strategies is reported in this text. · Abstract

Methods, data and reproducibility

Built 'Assembly Tools', a Juicebox module for spotting and fixing assembly errors interactively on Hi-C heatmaps, and used it with the automated 3D-DNA Hi-C scaffolding pipeline to assemble three mammalian genomes de novo from short-insert DNA-Seq and in situ Hi-C reads.

  • De novo genome assembly inputs (3.3Gb genome): short-insert Illumina DNA-Seq library plus in situ Hi-C library · wombat (Vombatus ursinus) · n = 300 million DNA-Seq reads + 100 million Hi-C reads
  • De novo genome assembly inputs (3.3Gb genome): short-insert Illumina DNA-Seq library plus in situ Hi-C library · Virginia opossum (Didelphis virginiana) · n = 300 million DNA-Seq reads + 100 million Hi-C reads
  • De novo genome assembly inputs (2.5Gb genome): short-insert Illumina DNA-Seq library plus in situ Hi-C library · raccoon (Procyon lotor) · n = 300 million DNA-Seq reads + 100 million Hi-C reads
Methods & tools
Juicebox, Juicebox Assembly Tools, 3D-DNA, in situ Hi-C, Illumina sequencing
Reproducibility gaps
Abstract only: no code or data availability statement, accession numbers, software versions or compute requirements appear in this text.
Limitations (2)
  • Only the abstract is available here, and it reports no contiguity, completeness or accuracy metrics, so the chromosome-length claim for the three assemblies cannot be assessed from this text. · noted in this summary
  • The cost advantage is not benchmarked against other assembly strategies in the abstract, and the amount of manual curation effort the point-and-click correction requires is not stated. · noted in this summary

Read this if you need chromosome-scale assemblies of large non-model genomes on a small budget and want an interactive way to inspect and correct Hi-C-based scaffolds.

Citations
313

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