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]