SYNOPSIS

DESCRIPTION

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]