start-asap

Initialize an ASA³P configuration file in Excel format (as required by ASA³P) from the command line. ASA³P is a fully featured bacterial assembly and analysis pipeline (paper).

Features

• Can prepare the ASA³P project directory in a non-interactive way
• Can use project metadata from a JSON file
• Command line parameters (like --genus Escherichia) will override JSON configuration(s)

Usage

start-asap -i READS_DIR -r REFERENCE -o OUTDIR [-p METADATA_JSON | -g GENUS -s SPECIES]

See the documentation page.

Installation

• Clone the repository and run start-asap, should work on most systems
• Install via BioConda with conda install -c bioconda start-asap

Output

The program can create an Excel file (config.xls) in the project directory, and optionally can copy the input files int he correct ./data subdirectory

The output file contains, as required two workbooks:

• Project

• Strains