AmpliconSuiteAggregator 6.0.0

Aggregator tool for multiple Amplicon Architect outputs

Amplicon Suite Aggregator

Description

Aggregates results from AmpliconSuite-pipeline runs.

• Accepts compressed input files (.tar.gz, .zip) of individual or grouped AmpliconSuite results, or plain directories.
• Aggregates and packages results into a new .tar.gz file, along with an aggregated .csv and .html summary.
• The output .tar.gz can be directly uploaded to AmpliconRepository.org.
• Supports batch sample renaming via a name map file.
• Can include auxiliary files alongside the upload; place them in a directory containing a file named AUX_DIR.

Installation

Option 1 — pip

pip install AmpliconSuiteAggregator

Option 2 — Git clone

git clone https://github.com/AmpliconSuite/AmpliconSuiteAggregator.git
cd AmpliconSuiteAggregator
pip install -r requirements.txt

Dependencies

Python packages: pandas, requests

Usage

python src/AmpliconSuiteAggregator.py -flist <input_list.txt> -o <project_name> [options]

input_list.txt is a plain text file with one input path per line (.tar.gz, .zip, or directory).

Aggregation options

Flag	Description
-flist FILE	Text file listing input paths, one per line
--files PATH [PATH ...]	Input files or directories directly on the command line
-o NAME	Output prefix / project name (required)
--name_map FILE	Two-column file: col 1 = current sample name, col 2 = replacement name. Applies a deep rename throughout all output files and tables.
-c {Yes,No}	Re-run Amplicon Classifier on inputs (Yes/No)
--ref GENOME	Reference genome: hg19, GRCh37, GRCh38, GRCh38_viral, or mm10

AmpliconRepository upload options

Flag	Description
-u EMAIL	AmpliconRepository username (email). If provided, triggers upload after aggregation.
--upload_only {Yes,No}	Skip aggregation and upload an existing .tar.gz directly
-s {prod,dev}	Target server (prod for most users)

Examples

Aggregate a set of results:

python src/AmpliconSuiteAggregator.py -flist input_list.txt -o MyProject

Aggregate and upload to AmpliconRepository:

python src/AmpliconSuiteAggregator.py -flist input_list.txt -o MyProject -u [e-mail] -s prod

Upload an already-aggregated file without re-aggregating:

python src/AmpliconSuiteAggregator.py --files MyProject.tar.gz -o MyProject -u [e-mail] --upload_only Yes -s prod

Authors

• Jens Luebeck (main contact)
• Thorin Tabor
• Edwin Huang

Issues

Bug reports and feature requests: GitHub Issues