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Citation & License

Citing PoolSeqFlow

The installed copy will print its own citation, with its version filled in:

./PoolSeqFlow cite

Use that rather than copying from here — it knows which version you have, and this page does not.

Which DOI to use

Zenodo issues two kinds of DOI, and the difference matters.

DOI What it identifies Use it for
10.5281/zenodo.19245611 All versions. Always resolves to the newest release Referring to PoolSeqFlow as a piece of software — a related-work mention, a README, a link
A version DOI, one per release One specific release, frozen Reporting results. This is the one a methods section needs

Cite the version you ran, not the newest one

Results depend on which release produced them. Filters, defaults and parameter names have all changed between versions — vcffilter.minDP went from having no effect to removing whole sites, and sample column ordering changed in 2.1.1. A paper citing the current release for numbers produced by an older one is describing a method it did not use.

Find the version that produced a given set of results in that project's Output/run_parameters.txt, which lists every release that has run there — ./PoolSeqFlow version tells you only what is installed now, which is not the same thing once you have upgraded. Then open the all-versions record and pick that version from the Versions list to get its DOI.

If more than one version is listed, the outputs were not all produced by the same release: completed steps are not redone on upgrade. Say so in your methods, or ./PoolSeqFlow reset and re-run under one version.

Reference

Kiratli, O. L. Z. (2026). PoolSeqFlow: A Nextflow pipeline for allele frequency analysis from pooled Illumina sequencing data (Version x.y.z) [Computer software]. https://doi.org/10.5281/zenodo.19245611

@software{kiratli_poolseqflow,
  author  = {Kiratli, Ozan L. Z.},
  title   = {PoolSeqFlow: A Nextflow pipeline for allele frequency
             analysis from pooled Illumina sequencing data},
  version = {x.y.z},
  year    = {2026},
  doi     = {10.5281/zenodo.19245611},
  url     = {https://github.com/ozankiratli/PoolSeqFlow}
}

Replace x.y.z with the version you ran, and swap the DOI for that version's own.

Citing the tools it runs

PoolSeqFlow orchestrates other people's software, and a methods section should credit it. The pipeline's own results depend directly on these:

Tool Used for
Nextflow Workflow execution
FastQC Read quality metrics, and the composition table driving clipping
Trim Galore Adapter and quality trimming
Cutadapt Composition-aware clipping
BWA Alignment (bwa mem)
SAMtools BAM processing, duplicate removal, filtering
BAMtools Alignment statistics
BCFtools Variant calling, normalisation, filtering
VCFtools Depth/quality filtering and SNP/INDEL splitting
SnpEff Variant annotation, if enabled

Exact versions are pinned in install/environment.yml, and the versions for the current release are listed under Requirements.

License

PoolSeqFlow is licensed under the Apache License 2.0.

The tools it invokes carry their own licenses, which are not affected by this one.

Contact

Ozan L. Z. Kiratli