Run mkCOInr

The scripts were written and tested on Linux. MacOS users will probably be able to run them. I suggest WSL for Windows users.

To run any of the scripts, open a terminal and type

perl PATH_TO_SCRIPTS/name_of_the_script.pl -argument_name argument_value

For example, if you are in the mkCOInr directory a command will look like this

perl scripts/dereplicate.pl -tsv custom/sequences_with_taxIDs.tsv -outdir custom/dereplicate -out custom_dereplicated_sequences.tsv

The list of arguments and options can be obtained by typing

perl PATH_TO_SCRIPTS/name_of_the_script.pl -help

For example:

perl scripts/download_taxonomy.pl -help