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).
- 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)
start-asap -i READS_DIR -r REFERENCE -o OUTDIR [-p METADATA_JSON | -g GENUS -s SPECIES]
See the documentation page.
- Clone the repository and run
start-asap
, should work on most systems - Install via BioConda with
conda install -c bioconda start-asap
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