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Citation

karyon is not archived anywhere yet. There is no Zenodo DOI and no CITATION.cff in the repository, so until there is, cite the repository and the version you used:

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

Record the version as well. karyon --version prints it for the command, and the Cargo.lock entry carries it for the library, together with the exact commit when the dependency comes from git, which it does until karyon is on crates.io. The version is worth recording because rendering is deterministic: the same input produces byte-identical output, so a figure can be regenerated exactly, but only against the version that drew it. A new default or a changed layout is a different figure from the same data.

If the figure is the finding rather than the illustration, say what the axis is. A stack of tracks is in genomic coordinates, a variable-site panel counts sites, an alignment counts columns and a squiggle counts samples, and "drawn with karyon" does not say which.

Authors

Paula Ruiz-Rodriguez and Mireia Coscolla, I²SysBio, University of Valencia-CSIC, FISABIO Joint Research Unit Infection and Public Health, Valencia, Spain.

Background

Most of what karyon draws is a standard representation, and the ones that are not have somebody else's idea in them. Those are worth citing in their own right when a figure leans on them.

Sequence logos scaled by information content are Schneider and Stephens's. LogoScore::InformationContent is that plot, and its fixed axis from zero to log2(K) is WebLogo's convention.

Schneider TD, Stephens RM. Sequence logos: a new way to display consensus sequences. Nucleic Acids Research. 1990;18(20):6097-6100.

Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: a sequence logo generator. Genome Research. 2004;14(6):1188-1190.

The enrichment and depletion logo, LogoTrack::edlogo, and the Dirichlet adaptive shrinkage behind LogoTrack::stabilize and the dash module, are both from the Logolas paper. The scoring schemes LogoScore offers follow the same source.

Dey KK, Xie D, Stephens M. A new sequence logo plot to highlight enrichment and depletion. BMC Bioinformatics. 2018;19:473.

Drawing only the columns that vary is the idea snipit is built around. The implementation in SnpTrack and the drawing are this crate's own.

The genome-wide significance threshold that genome_wide_threshold draws is -log10(5e-8), a Bonferroni correction for a million independent tests. It is a convention from human GWAS rather than a property of any particular study, and it is frequently the wrong number elsewhere. Cite whatever fixed the threshold you actually used.

Formats

karyon opens no files: karyon::read parses the line-based text formats a genomics shell already writes, and the caller decides where the text came from. Those formats are defined elsewhere:

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25(16):2078-2079.

Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R. The variant call format and VCFtools. Bioinformatics. 2011;27(15):2156-2158.

Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The Human Genome Browser at UCSC. Genome Research. 2002;12(6):996-1006.

BED, bedGraph and the cytoBand table come from the UCSC browser and are 0-based and half-open. GFF3, VCF, SAM and samtools depth are 1-based and inclusive. Both come out at the same place in the figure, and every reader has a test that pins a known base through the conversion.

The default nucleotide colours are IGV's, because a figure that recolours the bases surprises every reader.

Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP. Integrative Genomics Viewer. Nature Biotechnology. 2011;29(1):24-26.

License

MIT.

Next

  • Changelog, for what moved between the version cited and this one.
  • Contributing, for reporting a figure that came out wrong.