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

# correct\_abundances(1)

run the genome abundance similarity correction step

## NAME

correct\_abundances - run the genome abundance similarity correction step

## SYNOPSIS

**correct\_abundances** *NAMES*

## DESCRIPTION

Run the similarity correction step.

Note: Although it is possible to run the read mappers by hand or to create the similarity matrix manually, we strongly recommend to use the provided Python scripts 'run\_mappers.py' and 'create\_similarity\_matrix.py'.

## 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

- **-m** SMAT, **--similarity-matrix**=*SMAT*

  Path to similarity matrix file. The similarity matrix must be created with the same NAMES file. \[default: ./similarity\_matrix.npy\]

- **-s** SAM, **--samfiles**=*SAM*

  Pattern pointing to the SAM files created by the mapper. Placeholder for the name is "%s". \[default: ./SAM/%s.sam\]

- **-b** BOOT, **--bootstrap-samples**=*BOOT*

  Set the number of bootstrap samples. Use 1 to disable bootstrapping \[default: 100\]

- **-o** OUT, **--output**=*OUT*

  Plain text output file containing the results. \[default: ./results.txt\]