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]