correct_abundances1
Run the genome abundance similarity correction step
Usage
correct_abundances NAMES
Overview
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'.
Options
- 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]