AmpliconArchitect_reconstructions

This dataset contains the AmpliconArchitect (https://github.com/virajbdeshpande/AmpliconArchitect) output for reconstruction of amplicons from the following samples:1) 117 samples in "sample set 1" https://www.ncbi.nlm.nih.gov/bioproject/PRJNA338012/2) 18 samples which replicates of samples in sample set 13) 67 cervical samples from TCGA with HPV infection4) Amplicons from sample set 1 organized by various tags including: a) MultCluster, b) MultiChrom c) simple_cycles and d) BFB5) 7 samples reported by L'abbate et al 20146) 3 samples reported by Sanborn et al 2013 + 1 sample reported by Oesper et al 20127) 9 samples reported by Akagi et al 2013.1 summary file for each sample:_summary.txt - Summary of all amplicons reported in the sample.4 files per amplicon:graph.txt file: Breakpoint graph and copy numberscycles.txt file: Simple cycles in amplicon.png and .pdf: SV view of reconstruction.For viral amplicons from (3) and (7), 2 additional files (png and pdf) for each human interval connected to the viral genome..png and .cycles.txt files may be uploaded to http://genomequery.ucsd.edu:8800 for visualization and merging of cycles