Provided by: gasic_0.0.r19-4_amd64 bug


       correct_abundances - 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 ''.


       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]