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bioRxivBioinformaticsPreprint

SparK: A Publication-quality NGS Visualization Tool

Stefan KurtenbachiD, J. William HarbouriD

PDFDOICode

Abstract summary

Claude Opus 5.5 · xhigh effort · 18 Oct 2026 · from the abstract · CC BY-NC 4.0

Command-line Python tool that turns sequencing tracks into editable vector figures, averaging replicates, drawing standard-deviation tracks and marking significantly changed regions.

Exporting regions from IGV or the UCSC genome browser and assembling them into a figure is manual, and customising track appearance or overlaying replicates takes time. SparK builds the figure from a command line, so a changed region or track list only requires re-running the command.

Key results

  1. ClaimedSparK generates publication-ready, high-resolution true vector graphics directly from next-generation sequencing tracks, including RNA-seq, ChIP-seq and ATAC-seq.

    Stated as the tool's output; the abstract gives no figure examples, timings or comparison against IGV or the UCSC genome browser. · Abstract

  2. ClaimedThe feature set covers averaging of track replicates, plotting standard-deviation tracks and highlighting regions that changed significantly.

    Listed by the authors as novel functions of SparK; no worked example or statistical definition of a significant change is given. · Abstract

  3. ClaimedBecause figures are produced from command-line calls, changing the plotted genomic region or the set of tracks regenerates the figure in seconds, and the SVG output stays editable for text, lines and colours.

    Authors state regeneration happens "within seconds" without re-exporting and re-assembling; written in Python 3 and said to run on any major operating system. · Abstract

Methods, data and reproducibility

A Python 3 command-line program that reads next-generation sequencing track data and writes vector SVG figures, with options to average replicates, add standard-deviation tracks and highlight significantly changed areas.

Methods & tools
SparK, Python 3, IGV (Integrative Genomics Viewer), UCSC genome browser
Software & environment
Written in Python 3 and said to be executable on any major operating system.
Limitations (2)
  • Ease of use and speed are asserted rather than measured: no timing, no user study and no side-by-side comparison with IGV, the UCSC genome browser or other figure-assembly tools. · noted in this summary
  • No example dataset, input format specification or output figure is described in the available text, so the range of supported track types cannot be judged. · noted in this summary

Read this if you assemble genome-browser track figures for papers and want them scripted and regenerable as editable vector graphics.

Citations
69

Abstract

While there are sophisticated resources available for displaying NGS data, including the Integrative Genomics Viewer (IGV) and the UCSC genome browser, exporting regions and assembling figures for publication remains challenging. In particular, customizing track appearance and overlaying track replicates is a manual and time-consuming process. Here, we present SparK, a tool which auto-generates publication-ready, high-resolution, true vector graphic figures from any NGS-based tracks, including RNA-seq, ChIP-seq, and ATAC-seq. Novel functions of SparK include averaging of replicates, plotting standard deviation tracks, and highlighting significantly changed areas. SparK is written in Python 3, making it executable on any major OS platform. Using command line prompts to generate figures allows later changes to be made very easy. For instance, if the genomic region of the plot needs to be changed, or tracks need to be added or removed, the figure can easily be re-generated within seconds without the manual process of re-exporting and re-assembling everything. After plotting with SparK, changes to the output SVG vector graphic files are simple to make, including text, lines, and colors. SparK is publicly available on GitHub: https://github.com/harbourlab/SparK.

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