NAME
iva_qc_make_db - make a database as input for iva_qc
DESCRIPTION
usage: iva_qc_make_db [options] <output directory>
positional arguments:
- Directory_name
-
Name of output directory
options:
- -h, --help
-
show this help message and exit
- --add_to_ref Filename
-
Filename of Genbank IDs or GI numbers to be added to database. Format is: whitespace separated list of GI numbers on each line. One line defines one genome (e.g. flu is 8 segments, so put 8 GI numbers on one line for one flu reference)
- --skip_viruses
-
Do not run kraken-build --download-library viruses when building the database. If this option used, then --add_to_ref must also be used
- --threads INT
-
Number of threads to use [1]
- --minimizer_len INT
-
Number to pass to kraken-build minimizer_len option [13]
- --max_db_size INT
-
Number to pass to kraken-build max_db_size option [3]
- --verbose
-
Be verbose
- --version
-
show program's version number and exit