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bio-copy-number-focal-amplification-ecdna

Resolve the architecture of focal oncogene amplifications — extrachromosomal DNA (ecDNA), breakage-fusion-bridge (BFB) cycles, homogeneously staining regions (HSR), and linear amplification — from whole-genome sequencing with AmpliconArchitect, the AmpliconSuite pipeline, and AmpliconClassifier. Covers copy-number seed selection, breakpoint-graph reconstruction, balanced-flow optimization, ecDNA classification, and the limits of depth-only amplification calls. Use when a focal amplification needs structural characterization, when distinguishing ecDNA from chromosomal amplification, suspecting

BioTender-maxgithub.com/BioTender-maxGitHub ↗
claude-codeships scriptsNOASSERTION
Install
npx skills add BioTender-max/awesome-bio-agent-skills --skill focal-amplification-ecdna --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

Facts
Files in the skill folder: 3
SKILL.md size: 11 KB
Bundled scripts: yes
Path: skills/bioskills/focal-amplification-ecdna/SKILL.md
Open the folder on GitHub →
Where it comes from
Stars: 135
Language: Python

Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.

From the SKILL.md

## Version Compatibility Reference examples tested with: AmpliconSuite-pipeline 1.3+, AmpliconArchitect 1.3+, AmpliconClassifier 1.2+, CNVkit 0.9.10+, Python 3.10+, samtools 1.19+. Before using code patterns, verify installed versions match. If versions differ: - CLI: `AmpliconSuite-pipeline.py --help`, `amplicon_classifier.py --help` - AmpliconArchitect needs a `$AA_DATA_REPO` reference download and a Mosek license (free for academic use); confirm both are configured before running Verify the reference build — AmpliconArchitect was historically hg19-centric; GRCh38 support and data repos exist but the build must be set explicitly and consistently. # Focal Amplification and ecDNA **"This oncogene is amplified — but how, structurally"** -> A depth caller reports "high focal amplification" and stops. The biology depends entirely on the *architecture*: extrachromosomal DNA (ecDNA) behaves utterly differently from a chromosomal homogeneously staining region. Resolving architecture needs the breakpoint graph, not depth. - CLI: `AmpliconSuite-pipeline.py` (end-to-end), `AmpliconArchitect` (graph reconstruction), `AmpliconClassifier` (architecture call) - Input: WGS BAM plus copy-number s

What's inside
Steps it walks through
  1. Version Compatibility
  2. Why Architecture Matters — Four Amplicon Classes
  3. When to Suspect ecDNA
  4. The AmpliconSuite Workflow
  5. Failure Modes
  6. Garbage copy-number seeds produce garbage amplicons
  7. Calling ecDNA from depth alone
  8. Genome-build mismatch
  9. Short-read limits on complex amplicon resolution
  10. Inadequate coverage or FFPE input
  11. Reconciliation
  12. Quantitative Thresholds
  13. Common Errors
  14. References
Ships with 2 files
  • examples/run_ampliconsuite.sh
  • usage-guide.md
Commands it runs
AmpliconClassifier in sequence.
AmpliconSuite-pipeline.py \
table assigning each amplicon an architecture class.
CN above the seed threshold and to focal (not arm-level) size.
AmpliconSuite-pipeline.py -s sample_id -t 8 --bam tumor.bam --ref GRCh38 \
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About this skill
What does the bio-copy-number-focal-amplification-ecdna skill do?

Resolve the architecture of focal oncogene amplifications — extrachromosomal DNA (ecDNA), breakage-fusion-bridge (BFB) cycles, homogeneously staining regions (HSR), and linear amplification — from whole-genome sequencing with AmpliconArchitect, the AmpliconSuite pipeline, and AmpliconClassifier. Covers copy-number seed selection, breakpoint-graph reconstruction, balanced-flow optimization, ecDNA classification, and the limits of depth-only amplification calls. Use when a focal amplification needs structural characterization, when distinguishing ecDNA from chromosomal amplification, suspecting

How do I install it?

Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill focal-amplification-ecdna --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.

Where does this skill come from?

From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.

Is a popular skill a good skill?

Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.

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