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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 "quaqcr" in publications use:'
type: software
license: GPL-3.0-or-later
title: 'quaqcr: Quick ATAC-Seq QC'
version: 1.0.4
doi: 10.1093/bioinformatics/btae649
abstract: A wrapper around the 'quaqc' program described in Tremblay and Questa (2024)
  <https://doi.org/10.1093/bioinformatics/btae649>. 'quaqc' allows for assay for transposase-accessible
  chromatin using sequencing (ATAC-seq) specific quality control and read filtering
  of next-generation sequencing (NGS) data with minimal processing time and extremely
  low memory overhead. Any number of samples can be processed, using multiple threads
  if desired. 'quaqc' outputs a comprehensive set of aligned read metrics, including
  alignment size, fragment size, percent duplicates, mapq scores, read depth, GC content,
  and others. Although designed for ATAC-seq data, 'quaqc' can also be used for other
  unspliced DNA sequencing experiments (such as chromatin immunoprecipitation sequencing,
  or ChIP-seq) as many of the metrics are related to general sequencing quality. This
  R package also provides additional utilities for custom analyses and plotting of
  'quaqc' results.
authors:
- family-names: Tremblay
  given-names: Benjamin Jean-Marie
  email: benjmtremblay@gmail.com
  orcid: https://orcid.org/0000-0002-7441-2951
preferred-citation:
  type: article
  title: 'quaqc: efficient and quick ATAC-seq quality control and filtering'
  authors:
  - family-names: Tremblay
    given-names: Benjamin JM
  - family-names: Qüesta
    given-names: Julia I
  journal: Bioinformatics
  year: '2024'
  volume: '40'
  issue: '11'
  url: https://doi.org/10.1093/bioinformatics/btae649
  doi: 10.1093/bioinformatics/btae649
  start: btae649
repository: https://cran.r-universe.dev
repository-code: https://github.com/bjmt/quaqcr
commit: 7ce3663af461ac19d9db580a5eea23666670008f
url: https://github.com/bjmt/quaqcr
date-released: '2026-05-19'
contact:
- family-names: Tremblay
  given-names: Benjamin Jean-Marie
  email: benjmtremblay@gmail.com
  orcid: https://orcid.org/0000-0002-7441-2951