correct_abundances - run the genome abundance similarity
correction step
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'.
- 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]