This is the command correct_abundances that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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]
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