JU-works

JU SeqWorkbench Alpha

Sanger/FASTA sequence inspection, editing, grouping, visualization, and export in one local desktop workflow.

Independent personal development project

JU SeqWorkbench is developed independently as a personal software project. It is not an official product, service, software project, or development activity of my employer. The views, design choices, documentation, and development decisions presented on this site are my own.

JU SeqWorkbench Alpha is being developed for practical sequence-review work where sequence data has already been generated or prepared. The goal is to reduce repeated tool-switching between sequence inspection, editing, alignment review, grouping, mutation/variability analysis, visualization, and export.

It is not intended to replace large-scale NGS analysis platforms, read mapping, primary variant calling, or genome assembly pipelines.

September 2026 update: the first public 0.1.0-alpha will now be released after the main renderer bottleneck has been reduced enough for practical sequence review. The frozen pre-renderer baseline showed that residue coloring could take about 9.55 s on the 100 × 10,000 fixture, so the viewport-renderer work is being treated as the final pre-alpha engineering gate rather than an immediate post-release patch. The developer prototype now renders only visible rows/columns and has working Color/Dot display paths; production integration, editing parity, regression checks, and final manual validation are still in progress.

Why this project?

Routine Sanger/FASTA review can still involve moving between several tools for small but repeated tasks:

JU SeqWorkbench aims to connect those steps into one focused desktop workflow.

Workflow preview

Workflow preview

Current Alpha scope

The current 0.1.x workflow includes:

The analysis path is designed to use the current working sequence state rather than silently falling back to stale imported data.

Known Alpha limitations

The first alpha is still not intended to look or behave like a finished commercial release. However, the current plan is not to ship the known full-document renderer bottleneck unchanged.

The main limitations that will be stated openly with the release are:

The goal of the first public alpha is workflow validation: does the current sequence-review process save time, and which analysis/visualization views are actually worth improving next?

Performance baseline

A JU-only pre-renderer performance baseline has now been frozen before the planned renderer migration. It is intended as a development reference for later before/after optimization work, not as a ranking against other software.

The public baseline contains 5 synthetic alignment fixtures × 8 renderer metrics and reports median/min/max timings under the documented Windows/Qt test conditions.

View the Performance Baseline

Alpha → Beta → Full Release direction

The project roadmap is intentionally conservative. Post-alpha development is focused on improving the existing workflow before adding unrelated platform-scale features.

Interaction-network roadmap

The diagrams below are a visual interpretation of how the current modules interact and how the workflow may expand over time. Solid lines represent primary/strong workflow interactions; dotted lines represent weaker, supporting, or cross-module interactions.

Alpha — current interaction network

JU SeqWorkbench Alpha interaction network

Planned Beta interaction network

JU SeqWorkbench planned Beta interaction network

Possible Full Release interaction network

JU SeqWorkbench possible Full Release interaction network

Beta and Full Release diagrams are conceptual roadmaps. Their exact structure may change based on implementation results, alpha feedback, and workflow priorities.

Alpha — current foundation

FASTA / AB1 input
→ sequence review and editing
→ external MSA / alignment review
→ grouping / typing / similarity
→ point or region analysis
→ visualization / export

Beta — first post-alpha priorities

The current expected priorities are:

  1. Renderer follow-up and stabilization
    • continue tuning after the initial pre-alpha bottleneck fix
    • preserve the old renderer as a fallback/reference during early migration
    • tighten resize, selection/editing, and large-alignment edge cases based on Alpha feedback
  2. Visualization modernization
    • improve Point plots
    • improve Region plots
    • modernize mutation maps and summary layouts
    • make it easier to move from a visual pattern back to the underlying sequences
  3. Sequence relationship and tree inspection
    • NT/AA sequence relationship views
    • pairwise similarity/distance inspection
    • simple NJ/UPGMA-style distance-tree views
    • clade/subset selection linked back to the alignment workflow
  4. ORF- and segment-aware analysis
    • ORF mapping/selection
    • segment-level comparison
    • candidate homologous-region exploration
    • selection of comparable clades/ORFs/segments before detailed site analysis

Group-to-group comparison remains important, but is currently positioned after these first post-alpha priorities.

Toward a full release

The likely full-release direction is to integrate and stabilize the workflows that prove useful during alpha/beta testing:

Cloud collaboration, enterprise administration, large API ecosystems, and fully integrated AI analysis are not currently committed full-release requirements.

See the detailed roadmap

Sanger AB1 workflow

The AB1 workflow supports opening Sanger trace files, displaying chromatogram traces, reviewing the basecalled sequence, choosing original or reverse-complement orientation, trimming an import range, and bringing the selected sequence into the main viewer workflow.

External MSA

JU SeqWorkbench does not reimplement a multiple-sequence aligner. The alpha workflow connects to separately installed external aligners through temporary FASTA files and returns the aligned result to the viewer.

External aligner binaries are not bundled or automatically downloaded by the current alpha build.

Visualization and inspection

The visualization workflow deliberately separates two different questions:

The current plots are intended to validate the analysis workflow first. Visual hierarchy, comparison layouts, mutation maps, and publication/report-oriented presentation will be improved after real user feedback.

Feedback wanted

Feedback from people who review Sanger results, FASTA files, small MSA datasets, viral sequences, or amplicon sequence sets is especially useful.

Useful feedback includes:

If possible, describe what data should be compared and what you want to see from it.

Please do not upload confidential or unpublished sequence data publicly.

Development logs

Foundation

Analysis and visualization

Output, Sanger, and alpha preparation

Planned / upcoming development topics

The following areas are planned or under active exploration. Dedicated devlog pages will be linked when implementation and validation are mature enough to document clearly.

These are roadmap topics rather than promises for a specific release, and their order may change based on alpha feedback and implementation results.

Documentation

User guides

Project documentation

Please do not upload confidential or unpublished sequence data publicly.