DOKK / manpages / debian 12 / gasic / correct_abundances.1.en
CORRECT_ABUNDANCES(1) User Commands CORRECT_ABUNDANCES(1)

correct_abundances - run the genome abundance similarity correction step

correct_abundances NAMES

Run the similarity correction step.

Note: Although it is possible to run the read mappers by hand or to create the similarity matrix manually, we strongly recommend to use the provided Python scripts 'run_mappers.py' and 'create_similarity_matrix.py'.

Filename of the names file; the plain text names file should contain one name per line. The name is used as identifier in the whole algorithm.
show this help message and exit
Path to similarity matrix file. The similarity matrix must be created with the same NAMES file. [default: ./similarity_matrix.npy]
Pattern pointing to the SAM files created by the mapper. Placeholder for the name is "%s". [default: ./SAM/%s.sam]
Set the number of bootstrap samples. Use 1 to disable bootstrapping [default: 100]
Plain text output file containing the results. [default: ./results.txt]
February 2014 correct_abundances SVNr18