AmpliconSuite's repositories
AmpliconSuite-pipeline
A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect. Previously called PrepareAA.
AmpliconReconstructorOM
Reconstructs complex variation using Bionano optical mapping data and breakpoint graph data
AmpliconClassifier
Classify output of AmpliconArchitect to detect types of focal amplifications present
AmpliconArchitect
Identify one or more connected, focally amplified genomic regions to elucidate the architecture of focal amplifications such as ecDNA.
AmpliconSuiteAggregator
Aggregates the results from AmpliconSuite for upload to AmpliconRepository.org
AmpliconRepository
Website to host AmpliconSuite outputs, including AA outputs and resulting focal amplification classifications, such as ecDNA.
.github
Organization documentation
bioconda-recipes
Conda recipes for the bioconda channel.
ecSimulator
Simulate ecDNA structures with user-specified properties.
GenePatternFileDownloader
Utility script for downloading bam (or other file types) from GenePattern