correct_abundances(1) 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 '' and ''.


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]