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create_matrix - Online in the Cloud

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This is the command create_matrix 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


create_matrix - calculate the genome abundance similarity matrix

SYNOPSIS


create_matrix [options] NAMES

DESCRIPTION


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).

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

-s SIMULATOR, --simulator=SIMULATOR
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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