Project Structure

When you download a project or a selection of samples from AmpliconRepository, you receive a compressed archive (.tar.gz). This archive is organized by the AmpliconSuiteAggregator into a standardized structure designed for both human readability and programmatic analysis.

Root Directory: results/

The top-level directory contains the following key files:

  • aggregated_results.csv: A flat, tabular summary of all samples and features in the project. This is the best starting point for analyzing the dataset in Excel or R.
  • aggregated_results.html: A searchable, interactive HTML table of your results.
  • run.json: A machine-readable JSON file containing all metadata and relative file paths for the project.

Sample Data: samples/

The samples/ directory contains a subdirectory for every sample in the project. Inside each sample folder (e.g., samples/sample1/), you will find:

  • sample1_AA_results/: An uncompressed directory containing the raw output from AmpliconArchitect (AA), including:
    • *_summary.txt: A text summary of the amplicons found in the sample.
    • *_cycles.txt & *_graph.txt: The bioinformatic reconstructions of each amplicon.
    • *.pdf & *.png: Visualizations of the amplicon structures.
  • sample1_cnvkit_output.tar.gz: A compressed archive of the CNVkit results.
  • sample1_CNV_CALLS.bed: An uncompressed BED file containing the copy number calls used by AA.
  • Metadata & Logs:
    • sample1_run_metadata.json / sample1_sample_metadata.json
    • sample1.log: The pipeline execution log for this sample.
    • sample1_timing_log.txt: Performance metrics for the run.

Consolidated Analysis: consolidated_classification/

This directory aggregates results from AmpliconClassifier (AC) across all samples in the project, using the project name as a prefix. More about these files is available from the AC GitHub Readme.

  • *_result_table.tsv: The authoritative list of all focal amplifications identified across the project.
  • *_amplicon_classification_profiles.tsv: Detailed profiles for each identified amplicon.
  • *_gene_list.tsv: A comprehensive list of genes associated with each identified feature.
  • *_ecDNA_counts.tsv: Summary counts of ecDNA identified in the project.
  • *_ecDNA_context_calls.tsv: Data regarding the genomic context of identified ecDNA.
  • *_feature_basic_properties.tsv & *_feature_entropy.tsv: Metrics regarding the complexity and properties of identified features.
  • Subdirectories:
    • *_annotated_cycles_files/: Contains cycle files annotated with gene information.
    • *_classification_bed_files/: Contains BED files for each identified feature.
    • *_SV_summaries/: Summaries of structural variants associated with the features.

Other Files: other_files/

If you included supplementary data in an AUX_DIR during upload (e.g., FISH images, pathology reports), those files will be consolidated here.