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create_matrix - calculate the genome abundance similarity matrix


create_matrix [options] NAMES


Calculate the similarity matrix.

First, a set of reads is simulated for every reference genome using a read simulator from
core/tools.py specified via -s. Second, the simulated reads of each species are mapped
against all reference genomes using the mapper specified with -m. Third, the resulting
SAM-files are analyzed to calculate the similarity matrix. The similarity matrix is stored
as a numpy file (-o).


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

Identifier of read simulator defined in core/tools.py [default: none]

-r REF, --reference=REF
Reference sequence file pattern for the read simulator. Placeholder for the name is
"%s". [default: ./ref/%s.fasta]

-m MAPPER, --mapper=MAPPER
Identifier of mapper defined in core/tools.py [default: none]

-i INDEX, --index=INDEX
Reference index files for the read mapper. Placeholder for the name is "%s".
[default: ./ref/%s.fasta]

-t TEMP, --temp=TEMP
Directory to store temporary simulated datasets and SAM files. [default: ./temp]

-o OUT, --output=OUT
Output similarity matrix file. [default: ./similarity_matrix.npy]

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