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Citation

How to cite karyon and the version you used, who made it, and the methods and file formats it builds on, which deserve citing in their own right.

How to cite karyon

karyon does not have a DOI yet, so cite the repository together with the version you used:

Ruiz-Rodriguez P, Coscolla M. karyon: genomic track plots for Rust. PathoGenOmics Lab. https://github.com/PathoGenOmics-Lab/karyon

@misc{karyon,
  author       = {Ruiz-Rodriguez, Paula and Coscolla, Mireia},
  title        = {karyon: genomic track plots for Rust},
  howpublished = {PathoGenOmics Lab},
  url          = {https://github.com/PathoGenOmics-Lab/karyon},
  note         = {Version 0.14.0},
  year         = {2026}
}

Record the version

The library comes from git until it is on crates.io, so Cargo.lock records the exact commit your figures were drawn with:

[[package]]
name = "karyon"
version = "0.14.0"
source = "git+https://github.com/PathoGenOmics-Lab/karyon#<commit>"

Pin that commit in Cargo.toml to draw with it again later:

[dependencies]
karyon = { git = "https://github.com/PathoGenOmics-Lab/karyon", rev = "<commit>" }

karyon --version

karyon 0.14.0

The version matters because rendering is deterministic: the same input draws a byte-identical figure, so a figure can be regenerated exactly, but only with the version that drew it. A new default or a changed layout is a different figure from the same data.

Say what the axis counts

When the figure is the finding rather than an illustration, say in the caption what its horizontal axis counts. A stack of tracks counts positions on a sequence, a variable-site panel counts sites, an alignment counts columns, a domain panel counts residues and a squiggle counts samples, and "drawn with karyon" does not say which. See Coordinates.

Authors

Paula Ruiz-Rodriguez and Mireia Coscolla

I²SysBio, University of Valencia-CSIC, FISABIO Joint Research Unit Infection and Public Health, Valencia, Spain.

Methods it builds on

Most of what karyon draws is a standard representation, and the ones that are not carry somebody else's idea. When a figure leans on one of these, cite it as well.

What karyon draws Whose idea Reference
Sequence logos scaled by information content, LogoScore::InformationContent Schneider and Stephens; the axis fixed from zero to log2 of the alphabet size and the tallest symbol on top follow WebLogo [1], [2]
Enrichment and depletion logos, LogoTrack::edlogo, the other LogoScore schemes, and the shrinkage behind LogoTrack::stabilize and the dash module Logolas [3]
Only the columns that vary, SnpTrack the idea snipit is built around; the implementation and the drawing are karyon's own [4]
Model attribution drawn as the bases themselves, DynseqTrack the convention of BPNet and the dynseq browser track [5], [6]
The default base colours, BaseColors::conventional the IGV-style convention readers of genome figures already know: A green, C blue, G orange, T red [7]
The land under a Map Natural Earth's 1:110m land polygons, which are in the public domain Natural Earth

The genome-wide significance line that ManhattanTrack::genome_wide_threshold and --threshold genome-wide draw is -log10(5e-8), a Bonferroni correction for a million independent tests. It is a convention from human association studies rather than a property of any one study, and it is often the wrong number elsewhere: cite whatever fixed the threshold you actually used.

Formats it reads

The readers open no files: karyon::read parses the line-based text a genomics shell already writes, and the caller decides where the text came from. The formats themselves are defined elsewhere. How each one's coordinates are converted is on Coordinates.

Format Read by Reference
SAM --pileup, --split-reads [8]
VCF --variants, --structural [9]
BED, bedGraph, cytoBand --features, --loci, --coverage, --windows, --dynseq, --ideogram [10]
GFF3 --features, --loci, --clades the GFF3 specification
PAF, from minimap2 --synteny, --dotplot [11]
bedMethyl, from modkit --methylation modkit
Bismark methylation extractor output --bisulfite [12]
STAR SJ.out.tab --junctions [13]
InterProScan TSV --domains [14]
Gubbins recombination GFF --clades [15]
CNVkit .cns --copy-number [16]
ASCAT segments --copy-number [17]
NEXUS Tree::parse_nexus [18]
BLAST tabular output --links [19]

References

  1. Schneider TD, Stephens RM. Sequence logos: a new way to display consensus sequences. Nucleic Acids Research. 1990;18(20):6097-6100. doi:10.1093/nar/18.20.6097
  2. Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: a sequence logo generator. Genome Research. 2004;14(6):1188-1190. doi:10.1101/gr.849004
  3. Dey KK, Xie D, Stephens M. A new sequence logo plot to highlight enrichment and depletion. BMC Bioinformatics. 2018;19:473. doi:10.1186/s12859-018-2489-3
  4. O'Toole Á, Aziz A, Maloney D. Publication-ready single nucleotide polymorphism visualization with snipit. Bioinformatics. 2024;40(8):btae510. doi:10.1093/bioinformatics/btae510
  5. Avsec Ž, Weilert M, Shrikumar A, Krueger S, Alexandari A, Dalal K, et al. Base-resolution models of transcription-factor binding reveal soft motif syntax. Nature Genetics. 2021;53(3):354-366. doi:10.1038/s41588-021-00782-6
  6. Nair S, Barrett A, Li D, Raney BJ, Lee BT, Kerpedjiev P, et al. The dynseq browser track shows context-specific features at nucleotide resolution. Nature Genetics. 2022;54(11):1581-1583. doi:10.1038/s41588-022-01194-w
  7. Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, et al. Integrative genomics viewer. Nature Biotechnology. 2011;29(1):24-26. doi:10.1038/nbt.1754
  8. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25(16):2078-2079. doi:10.1093/bioinformatics/btp352
  9. Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, et al. The variant call format and VCFtools. Bioinformatics. 2011;27(15):2156-2158. doi:10.1093/bioinformatics/btr330
  10. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, et al. The human genome browser at UCSC. Genome Research. 2002;12(6):996-1006. doi:10.1101/gr.229102
  11. Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018;34(18):3094-3100. doi:10.1093/bioinformatics/bty191
  12. Krueger F, Andrews SR. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics. 2011;27(11):1571-1572. doi:10.1093/bioinformatics/btr167
  13. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15-21. doi:10.1093/bioinformatics/bts635
  14. Jones P, Binns D, Chang HY, Fraser M, Li W, McAnulla C, et al. InterProScan 5: genome-scale protein function classification. Bioinformatics. 2014;30(9):1236-1240. doi:10.1093/bioinformatics/btu031
  15. Croucher NJ, Page AJ, Connor TR, Delaney AJ, Keane JA, Bentley SD, et al. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Research. 2015;43(3):e15. doi:10.1093/nar/gku1196
  16. Talevich E, Shain AH, Botton T, Bastian BC. CNVkit: genome-wide copy number detection and visualization from targeted DNA sequencing. PLoS Computational Biology. 2016;12(4):e1004873. doi:10.1371/journal.pcbi.1004873
  17. Van Loo P, Nordgard SH, Lingjærde OC, Russnes HG, Rye IH, Sun W, et al. Allele-specific copy number analysis of tumors. Proceedings of the National Academy of Sciences of the USA. 2010;107(39):16910-16915. doi:10.1073/pnas.1009843107
  18. Maddison DR, Swofford DL, Maddison WP. NEXUS: an extensible file format for systematic information. Systematic Biology. 1997;46(4):590-621. doi:10.1093/sysbio/46.4.590
  19. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: architecture and applications. BMC Bioinformatics. 2009;10:421. doi:10.1186/1471-2105-10-421

Licence

karyon is released under the MIT licence, copyright 2026 Paula Ruiz-Rodriguez and Mireia Coscolla. A plotting library is meant to be a dependency, and a permissive licence lets any tool depend on it whatever that tool's own licence is.

Where next

  • Changelog

    What moved between the version you cited and this one.

  • Contributing

    How to report a figure that came out wrong, and what a change has to pass.