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BOLDigger as a command-line tool

Project description


BOLDigger as a command-line tool for easy implementation into bioinformatic pipelines.

Before using please check that you have updated to the latest version of BOLDigger since BOLDigger-cline heavily relies on the current code of BOLDigger.

For a detailed explanation of the different functions BOLDigger offers please visit:


BOLDigger-commandline requires Python version 3.6 or higher and can be easily installed by using pip in any command line:

pip install boldigger_cline

will install BOLDigger-commandline as well as all needed dependencies.

To update BOLDigger-commandline type:

pip install --upgrade boldigger_cline

How to cite

Buchner D, Leese F (2020) BOLDigger – a Python package to identify and organise sequences with the Barcode of Life Data systems. Metabarcoding and Metagenomics 4: e53535.


BOLDigger commandline offers all functions of BOLDigger as a command line tool.

For documentation on how to use type:

boldigger-cline -h


usage: boldigger-cline [-h] [--version]

BOLDigger as a command line tool,


positional arguments:
    ie_coi              COI identification engine
    ie_its              ITS identification engine
    ie_rbcl             rbcl identification engine
    add_metadata        additional data download
    first_hit           use the first hit as top hit
    jamp_hit            determine the top hit with the JAMP method
    digger_hit          determine the top hit with the BOLDigger method

optional arguments:
  -h, --help            show this help message and exit
  --version             show program's version number and exit

The help function also works for all sub-functions of BOLDigger-commandline:

boldigger-cline ie_coi -h


usage: boldigger-cline ie_coi [-h]
                              username password fasta_path output_folder


positional arguments:
  username       Username for boldsystems login
  password       Password for boldsystems login
  fasta_path     Path to the fasta file to be blasted
  output_folder  Path to the output folder
  batch_size     Batch size to be blasted.

optional arguments:
  -h, --help     show this help message and exit

Identification engine - Example usage

To run the identification engine for COI type:

boldigger-cline ie_coi username password fasta_path output_folder [batch size](optional)

Additional data download and top hit determination

All other function of BOLDigger commandline just need a filepath to the BOLDResult file as an argument.

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