Installation

Special attention was taken to minimize dependencies.

Third-party programs

The following tools should be installed. (Scripts using the program are in parentheses)

• nsdpy used for downloading sequences from NCBI (Hebert and Meglécz, 2022)

• BLAST (Altschul et al., 1997; format_bold.pl, for the check_orientation option, format_db.pl for the blast option)

• vsearch (Rognes et al., 2016; dereplicate.pl, pool_and_dereplicate.pl, select_region.pl)

• cutadapt (Martin, 2011; select_region.pl for the e_pcr option)

• wget (download_bold.pl, download_taxonomy.pl)

All third-party programs can be easily installed to a conda environment, but it is not essential to use conda.

Commands for a quick installation of the conda environment and dependencies:

conda create --name mkcoinr python=3.9 -y
conda activate mkcoinr

python3 -m pip install cutadapt
conda install -c bioconda blast -y
conda install -c bioconda vsearch -y
pip install nsdpy

wget is installed by default in Linux systems. It can be installed on MacOS either by conda or brew

conda install wget

brew install wget

mkCOInr scripts

The mkCOInr scripts are written in Perl, no installation is necessary to run them apart from the Perl interpreter already installed in all unix systems. Just clone the mkCOInr git repository and you are ready.