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# CITATION 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 "piglet" in publications use:'
type: software
license: CC-BY-SA-4.0
title: 'piglet: Program for Inferring Immunoglobulin Allele Similarity Clusters and
  Genotypes'
version: 1.2.0
doi: 10.1093/nar/gkad603
identifiers:
- type: doi
  value: 10.32614/CRAN.package.piglet
abstract: Improves genotype inference and downstream Adaptive Immune Receptor Repertoire
  Sequence data analysis. Inference of allele similarity clusters, an alternative
  naming scheme and genotype inference for immunoglobulin heavy chain repertoires.
  The main tools are allele similarity clusters, and allele based genotype. The first
  tool is designed to reduce the ambiguity within the immunoglobulin heavy chain V
  alleles. The ambiguity is caused by duplicated or similar alleles which are shared
  among different genes. The second tool is an allele based genotype, that determined
  the presence of an allele based on a threshold derived from a naive population.
  See Peres et al. (2023) <https://doi.org/10.1093/nar/gkad603>.
authors:
- family-names: Peres
  given-names: Ayelet
  email: ayelet.peres@yale.edu
- family-names: Lees
  given-names: William
  email: william@lees.org.uk
- family-names: Yaari
  given-names: Gur
  email: gur.yaari@yale.edu
preferred-citation:
  type: article
  title: IGHV allele similarity clustering improves genotype inference from adaptive
    immune receptor repertoire sequencing data
  authors:
  - family-names: Peres
    given-names: Ayelet
    email: ayelet.peres@yale.edu
  - family-names: Lees
    given-names: William
    email: william@lees.org.uk
  - family-names: Rodriguez
    given-names: Oscar
  - family-names: Lee
    given-names: Noah
  - family-names: Polak
    given-names: Pazit
  - family-names: Hope
    given-names: Ronen
  - family-names: Kedmi
    given-names: Meirav
  - family-names: Collins
    given-names: Andrew
  - family-names: Ohlin
    given-names: Mats
  - family-names: Kleinstein
    given-names: Steven
  - family-names: Watson
    given-names: Corey
  - family-names: Yaari
    given-names: Gur
    email: gur.yaari@biu.ac.il
  year: '2023'
  doi: 10.1093/nar/gkad603
  journal: Nucleic Acid Research
  issue: '51'
  start: E86
repository: https://ayeletperes.r-universe.dev
commit: 6e9ecb1b3f26f45c6826b737502617200d4180a1
date-released: '2026-02-17'
contact:
- family-names: Peres
  given-names: Ayelet
  email: ayelet.peres@yale.edu