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A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect. Previously called PrepareAA.
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.
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
ecc_caller is a pipeline designed to take Illumina NovaSeq paired end sequencing reads generated from isolated circular DNA and call eccDNA forming regions.
Scripts and analysis for the Giurgiu et al. 2024. Genome Research. "Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data using Decoil".
A Snakemake workflow for creating testing data for ecDNA analysis workflows: long reads (Nanopore with NanoSim) and short reads (Illumina with seqkit and mason).