# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "polyRAD" in publications use:'
type: software
license: GPL-2.0-or-later
title: 'polyRAD: Genotype Calling with Uncertainty from Sequencing Data in Polyploids
  and Diploids'
version: 2.0.0.9003
doi: 10.1534/g3.118.200913
identifiers:
- type: doi
  value: 10.32614/CRAN.package.polyRAD
abstract: Read depth data from genotyping-by-sequencing (GBS) or restriction site-associated
  DNA sequencing (RAD-seq) are imported and used to make Bayesian probability estimates
  of genotypes in polyploids or diploids. The genotype probabilities, posterior mean
  genotypes, or most probable genotypes can then be exported for downstream analysis.
  'polyRAD' is described by Clark et al. (2019) <https://doi.org/10.1534/g3.118.200913>,
  and the Hind/He statistic for marker filtering is described by Clark et al. (2022)
  <https://doi.org/10.1186/s12859-022-04635-9>. A variant calling pipeline for highly
  duplicated genomes is also included and is described by Clark et al. (2020, Version
  1) <https://doi.org/10.1101/2020.01.11.902890>.
authors:
- family-names: Clark
  given-names: Lindsay V.
  email: Lindsay.Clark@seattlechildrens.org
  orcid: https://orcid.org/0000-0002-3881-9252
preferred-citation:
  type: article
  title: 'polyRAD: Genotype calling with uncertainty from sequencing data in polyploids
    and diploids'
  authors:
  - family-names: Clark
    given-names: Lindsay V.
    email: lvclark@illinois.edu
    orcid: https://orcid.org/0000-0002-3881-9252
  - family-names: Lipka
    given-names: Alexander E.
    email: alipka@illinois.edu
  - family-names: Sacks
    given-names: Erik J.
    email: esacks@illinois.edu
  journal: G3
  year: '2019'
  volume: '9'
  issue: '3'
  doi: 10.1534/g3.118.200913
  start: '663'
  end: '673'
repository: https://polyploids.r-universe.dev
repository-code: https://github.com/lvclark/polyRAD
commit: 6edf95b72ebf6962cc841fb9e6f089777029e6aa
url: https://github.com/lvclark/polyRAD
date-released: '2023-12-16'
contact:
- family-names: Clark
  given-names: Lindsay V.
  email: Lindsay.Clark@seattlechildrens.org
  orcid: https://orcid.org/0000-0002-3881-9252
references:
- type: article
  title: A population-level statistic for assessing Mendelian behavior of genotyping-by-sequencing
    data from highly duplicated genomes
  authors:
  - family-names: Clark
    given-names: Lindsay V.
    email: lvclark@illinois.edu
  - family-names: Mays
    given-names: Wittney
    email: wittney2@illinois.edu
  - family-names: Lipka
    given-names: Alexander E.
    email: alipka@illinois.edu
  - family-names: Sacks
    given-names: Erik J.
    email: esacks@illinois.edu
  journal: BMC Bioinformatics
  year: '2022'
  volume: '23'
  doi: 10.1186/s12859-022-04635-9
  start: '101'