A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect. Previously called PrepareAA.
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Feb 11, 2025 - Python
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ecdna
Here are 17 public repositories matching this topic...
A method for circular DNA detection based on probabilistic mapping of ultrashort reads
ngs circrna structural-variation circrna-prediction genotyping circrnas eccdna ecdna circular-dna microdna
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Jul 17, 2024 - Python
Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other eukaryotic cells.
workflow pipeline genomics nextflow dna circular nf-core extrachromosomal-circular-dna eccdna ecdna ampliconarchitect circle-seq ampliconsuite
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Jan 27, 2025 - Python
GCAP (Gene-level Circular Amplicon Prediction) firstly implements extrachromosomal DNA detection from whole-exome-sequencing (WES) data and absolute copy number profiles. https://shixiangwang.r-universe.dev/gcap
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Jan 6, 2025 - R
Classify output of AmpliconArchitect to detect types of focal amplifications present
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Jan 30, 2025 - Python
Reconstructs complex variation using Bionano optical mapping data and breakpoint graph data
python ngs cancer-genomics genome-sequencing genome-analysis genome-assembly optical-mapping bionano ecdna
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Nov 13, 2023 - Python
Tool used to quantify extrachromosomal DNA (ecDNA) in metaphase images stained with DAPI and FISH probes.
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Apr 27, 2024 - Python
Identify one or more connected, focally amplified genomic regions to elucidate the architecture of focal amplifications such as ecDNA.
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Dec 12, 2024 - Python
ecc_caller is a pipeline designed to take Illumina NovaSeq paired end sequencing reads generated from isolated circular DNA and call eccDNA forming regions.
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Mar 10, 2023 - Python
Visualize circular ecDNA reconstructions using Decoil-viz
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Jan 24, 2025 - Python
Scripts and analysis for the Giurgiu et al. 2024. Genome Research. "Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data using Decoil".
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Oct 14, 2024 - Jupyter Notebook
Simulation of ecDNA sequence templates
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Aug 9, 2024 - Python
Wraps the AmpliconSuite-pipeline workflow to identify one or more connected genomic regions which have copy number amplifications.
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Dec 17, 2024 - Python
Website to host AmpliconSuite outputs, including AA outputs and resulting focal amplification classifications, such as ecDNA.
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Feb 27, 2025 - JavaScript
A Snakemake workflow for creating testing data for ecDNA analysis workflows: long reads (Nanopore with NanoSim) and short reads (Illumina with seqkit and mason).
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Feb 12, 2025 - Python
Simulate ecDNA structures with user-specified properties.
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Jan 27, 2025 - Python
Evolutionary models of extrachromosomal DNA (ecDNA).
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Aug 1, 2024 - Rust
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