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# CITATION.cff file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "karioCaS" in publications use:'
type: software
license: GPL-3.0-or-later
title: 'karioCaS: Kraken Confidence Scores for Reliable Domain-Specific Microbiota
  Inference and Discovery'
version: 0.99.16
abstract: Provides a comprehensive framework for analyzing Kraken2 metagenomic classification
  using multiple confidence scores. karioCaS implements a robust comparative approach
  to evaluate taxonomic stability across different stringency levels, facilitating
  the identification of reliable microbiota components and the discovery of potentially
  novel or unrepresented species. A key innovation is its domain-specific analysis,
  separately processing Bacteria, Archaea, Eukaryota, and Viruses to ensure balanced
  visibility of all biological domains. Includes high-quality visualization tools
  for retention rates, shared taxa (Upset plots), and stability heatmaps.
authors:
- family-names: Parente
  given-names: Thiago
  email: thiago.parente@fiocruz.br
  orcid: https://orcid.org/0000-0001-7501-726X
repository: https://bioc.r-universe.dev
repository-code: https://github.com/thiagoparentefiocruz/karioCaS
commit: f2bbabd144ef4c6428e1c42253f83231c592ce6c
url: https://github.com/thiagoparentefiocruz/karioCaS
date-released: '2026-09-28'
contact:
- family-names: Parente
  given-names: Thiago
  email: thiago.parente@fiocruz.br
  orcid: https://orcid.org/0000-0001-7501-726X