chromosomix

A unified genome browser for multi-dimensional genomic data. Chromatin contact maps, genome tracks and 3D models, side by side, straight from your files.

chromosomix launches in about a second and reads your data where it lives, on your own disk or in the cloud. No server, no preprocessing, no installation, no account, and it works offline. Most formats open as they are: .*cool, .hic, HiC-Pro, .pairs, bigWig, BED, BAM, FASTA/.2bit, 3D structures and more.

Main features

• Support for all genomic data types:

  • Supports 1D genomic formats: bigWig, bigBed, BED, bedGraph, wig, GTF/GFF3, FASTA (+.fai), .2bit, BAM, VCF, barChart/bigBarChart, genePred/refFlat/bigGenePred, bedMethyl/bigMethyl, chrom.sizes, ...
  • Supports 2D genomic formats: .*cool, .hic, HiC-Pro, pairs(.gz), ..., at every resolution the file stores. A .pairs is binned on import, and the same pass counts what pairtools stats counts — mapped, duplicates, cis and trans, pair types, strand convergence, library size — shown in the General panel and saved as a .stats file MultiQC reads. Also supports interaction formats: BEDPE, and UCSC's interact/bigInteract and longrange/longTabix — drawn as arcs over the contact map and as their own lane in the 1D browser.
  • Supports 3D genomic formats: WashU's g3d (text or binary), .3dg, and bed3d, drawn in 3D and synchronized with the maps and tracks view. Every model also leaves as a PDB for PyMOL, ChimeraX and the other molecular viewers, a chain per chromosome and bonds along the fibre, and reads back here.

• Perform analyses directly in the browser:

  • 1D analysis tasks: peak calling from a coverage track (yapc, with IDR between replicates), motif search, base composition and GC skew, the origin and terminus of replication, metaplots, track correlation, FRiP over a feature set, signal by group, interval overlap with a shuffle null, ...
  • 2D analysis tasks: a QC map report (one HTML page, and MultiQC sections from the CLI), P(s) (and its four pair orientations), scalogram, diamond insulation, directionality index, HiC score, TAD annotation (Juicer's Arrowhead), coverage, cis/trans per chromosome, virtual 4C, compartments annotation and saddle plot, the alignment of a bacterial chromosome's two arms, loops and borders detection, APA, loop ranking, ...
  • 3D analysis tasks: build a 3D model from the contact map (pastis-NB or ShRec3D), compare a 3D model with the contact map, and turn a 3D model into tracks.

• Serverless browser & CLI-based: there is no upload, no required preprocessing step and no backend of any kind — the viewer is static files that read standard genome-wide formats directly. Every analysis can be run interactively, in the browser, or programmatically, with the chromosomix command line in a script or a pipeline: the same tasks, with the same parameters, producing the same results. A bottom Console panel in the browser records every run and reports the chromosomix command that repeats it.

• Dedicated browser panels, four around the picture:

  • General panel: the file itself — its attributes, its chromosomes (or a metagenome's genomes and contigs), a minimap of the genome and the metadata it stores.
  • Aesthetics panel: to customize scales, color map, normalization, track layout, grouping, ...
  • Annotations panel, supporting linear tracks, 1D and 2D manual annotations, bookmarks and synthetic annotations.
  • Analysis panel: runs the analyses above on what is on screen, with exportable results.

• Virtual file system: The browser runs entirely in the client, with no server-side processing or data upload. It uses a virtual file system to access local files, remote files, and cloud storage:

  • Cloud-based file access: Open files directly from any object store that serves byte ranges with CORS (e.g. S3, Cloudflare R2, Google Cloud Storage, or any HTTP server that supports range requests), from Dropbox and Google Drive share links, and private Google Drive folder or Dropbox.
  • Stores: several pre-configured remote data stores are available — the lab's own figures, IGV's genomes, 4DN open data, ENCODE, DNA Zoo and Roadmap — and so is any UCSC track hub with a hub.txt file. The user can also setup their own store by providing a structured JSON file describing the store and its data.

• Side by side: contact maps, 1D browsers and 3D models open as the cells of a deck, panned and zoomed together, and several sessions stay open at once, one tab each.

Philosophy

1. No backend or install of any kind. No tile server, no specific process on a host, no accounts. The viewer is static files; the data are objects on a bucket, or a file on your disk. This is what makes the app free to run and free to archive.

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