---
name: "create_matrix"
section: "1"
platform: "linux"
package: "gasic"
version: "0.0.r19-8"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/create_matrix"
---

# create\_matrix(1)

calculate the genome abundance similarity matrix

## 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. \[default: ./similarity\_matrix.npy\]