bio-copy-number-focal-amplification-ecdna

Name: bio-copy-number-focal-amplification-ecdna
Rating: 5 (1 reviews)
Author: bg-szy

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 c

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Updated 14 days ago

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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

How to add

Drop this on your repo README

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Version Compatibility

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