Provided by: gasic_0.0.r19-4_amd64
correct_abundances - run the genome abundance similarity correction step
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'.
NAMES: 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. -h, --help show this help message and exit -m SMAT, --similarity-matrix=SMAT Path to similarity matrix file. The similarity matrix must be created with the same NAMES file. [default: ./similarity_matrix.npy] -s SAM, --samfiles=SAM Pattern pointing to the SAM files created by the mapper. Placeholder for the name is "%s". [default: ./SAM/%s.sam] -b BOOT, --bootstrap-samples=BOOT Set the number of bootstrap samples. Use 1 to disable bootstrapping [default: 100] -o OUT, --output=OUT Plain text output file containing the results. [default: ./results.txt]