Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

By Neva C. Durand, James T. Robinson, Muhammad Saad Shamim, Ido Machol, Jill P. Mesirov, Eric S. Lander, Erez Lieberman Aiden. Cell Systems, 2016

2,078 citations recorded by the source corpus.

Hi-C experiments study how genomes fold in 3D, generating contact maps containing features as small as 20bp and as large as 200-Mb. Here we introduce Juicebox, a tool for exploring Hi-C and other contact map data. Juicebox allows users to zoom in and out of Hi-C maps interactively, just as a user of Google Earth might zoom in and out of a geographic map. Maps can be compared to one another, or to 1D tracks or 2D feature sets.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/7162b2582ce0f75564b4b290a2e205e58ed974b6

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Citations in the corpus

Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data (2017, positive): “Juicebox.js is designed to work with data in the hic format (Durand et al., 2016a), a compressed indexed format that enables fast queries and can be used with a wide variety of contact mapping experiments, such as dilution Hi-C (Lieberman-Aiden et al., 2009), in situ Hi-C (Rao et al., 2014),…”
Significantly improving the quality of genome assemblies through curation (2020, neutral): “these tend to analyse a single data type at a time rather than combining insights from analysis of several in parallel [8,9].”
Cohesin loss eliminates all loop domains (2017, methodology): “We first annotated loops in our maps for auxin-treated RAD21-mAC cells using default HiCCUPS parameters for 5,10, and 25kb resolutions (Durand et al., 2016b; Rao et al., 2014) with the additional requirement that the peak pixel show less than 4.5-fold enrichment over local expecteds (in order to…”
Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments (2016, positive): “In addition, Juicer is available on the cloud at Amazon Web Services, and the test data used to review this paper is available at http://dx.doi.org/10.17632/c6bg4cbggn.1.”
The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000 (2018, methodology): “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).”
Integrating Hi-C links with assembly graphs for chromosome-scale assembly (2018, methodology): “For 3D-DNA, alignments were generated using the Juicer alignment pipeline (Durand et al., 2016b) with defaults (-m haploid -t 15000 -s 2), except for mis-assembly detection, as listed.”
De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds (2016, methodology): “quinquefasciatus allowed us to use our Hi-C data to create a Hi-C heatmap showing proximity relationships between chromosomal loci throughout both genomes (22, 23) (Figs.”
New developments on the Encyclopedia of DNA Elements (ENCODE) data portal (2019, methodology): “…of Hi-C re-sults, portal pages for these experiments were modified to include links, which can be found on the ‘File details’ tab, redirecting to the Juicebox visualization software web page (https://aidenlab.org/juicebox/) and to allow selection of the relevant files for visualization (30,31).”
The UCSC Genome Browser database: 2021 update (2020, methodology): “Hi-C data from custom tracks and track hubs can also be visualized (40,44,45).”