Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add GPTomics/bioSkills --skill sashimi-plotsgit clone --depth 1 https://github.com/GPTomics/bioSkillsWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/gptomics/bioskills/sashimi-plots)<a href="https://agentmods.dev/skills/gptomics/bioskills/sashimi-plots"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/sashimi-plots/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/gptomics/bioskills/sashimi-plots"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/sashimi-plots.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00160 | $0.05009 |
| Opus 5 | $0.00080 | $0.02505 |
| Sonnet 5 | $0.00032 | $0.01002 |
| Haiku 4.5 | $0.00016 | $0.00501 |
Grade A, and why
bio-sashimi-plots scanned grade A with 1 finding against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 9d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Runs shell commandslowCapability
Expected in a hook, worth knowing in a rule or an instructions file.
subprocess.run([ Copies of this mod
1 near-identical copy found in the catalogue:
- bio-sashimi-plots — 95% identical, 12 lines differ
How it starts
The opening of the file, as written. The whole thing — 392 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: ggsashimi 1.1+, rmats2sashimiplot 3.0+, MAJIQ 3.0+, leafcutter 0.2.9+, pyGenomeTracks 3.8+, ggplot2 3.5+, pandas 2.2+
Before using code patterns, verify installed versions match. If versions differ:
- Python:
pip show <package>thenhelp(module.function)to check signatures - CLI:
<tool> --versionthen<tool> --helpto confirm flags
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
Sashimi Plot Visualization
Visualize RNA-seq coverage tracks with splice junction arcs labeled by read count. Sashimi plots originated with MISO (Katz 2010 Nat Methods); modern tools differ in input handling, group aggregation logic, and customization. Tool choice is not interchangeable — some tools work only with specific upstream output formats.
Tool Selection Matrix
| Tool | Best for | Input | Strengths | Fails when |
|---|---|---|---|---|
| ggsashimi | Publication-quality grouped overlays from any BAM | BAMs + region | --overlay aggregates samples within a group; clean PDFs |
No native rMATS/MAJIQ integration; need to extract coords manually |
| rmats2sashimiplot | One-line plot from rMATS output | rMATS event file + BAMs | No manual coord extraction | rMATS-specific; doesn't handle leafcutter or MAJIQ |
| MAJIQ-VOILA | Interactive LSV browsing with posterior PSI distributions | MAJIQ build + psi/deltapsi | Splice-graph topology; LSV-aware; posterior violins | Static figures; non-academic license |
| leafviz | Cluster-level interactive browsing with NMD annotation | leafcutter differential output | Filter table + sashimi-like plots; NMD-aware | leafcutter-specific |
| Jutils | Unified output across rMATS, leafcutter, MntJULiP, MAJIQ | Tool-specific differential output | Heatmaps, Venn, sashimi tool-agnostically | Output less polished than ggsashimi |
| pyGenomeTracks | Multi-track publication figures (RNA-seq + ChIP/ATAC) | BigWig + BED + GTF | Combine RNA with chromatin tracks | Not splicing-specific; configure tracks manually |
| IGV (interactive) | Quick ad-hoc inspection | BAM + region | Scrollable, instant | Not for publication figures |
| MISO sashimi | Historical | MISO output | Original sashimi format | MISO unmaintained; no longer recommended |
What ships with it
2 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 9d ago First seen · 392 lines · 160 tokens per session scan A c2100d58739a
bio-sashimi-plots is a skill published in the GitHub repository GPTomics/bioSkills (1,199 stars, last pushed 24d ago), licensed MIT. It adds 160 tokens to every session and 5,009 once invoked, about $0.0008 per session on Opus 5. A static security scan graded it A with 1 finding (runs shell commands). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
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