NAME¶

correct_abundances - run the genome abundance similarity correction step

SYNOPSIS¶

correct_abundances NAMES

DESCRIPTION¶

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]