Resources

Standards, support links, reproducibility guidance, citations, and example data for breeding and genomic analysis.

Use this page when you need a primary specification, a support route, or a checklist to make an analysis easier to reproduce. For explanations and worked examples, use the Learn library. For installation and package documentation, start with Software.

NoteBreeding Insight Learning Hub

The Breeding Insight Learning Hub brings together additional manuals, training materials, videos, and resources for Breeding Insight tools and services.

Get Help

Report software problems in the repository that owns the code. Search existing issues first, then include the software version, operating system, the step that failed, and the complete error message.

Software Issue tracker
AlloMate Breeding-Insight/AlloMate issues
BIGapp Breeding-Insight/BIGapp issues
BIGpopA Breeding-Insight/BIGpopA issues
BIGr Breeding-Insight/BIGr issues
Familia Breeding-Insight/Familia issues
Qploidy2 Breeding-Insight/Qploidy2 issues
WarningProtect Private Data

Do not attach private genotype files, phenotypes, pedigrees, sample identifiers, or breeding-program records to a public issue. Create a small simulated or de-identified example when the error cannot be reproduced with package example data.

For workshop questions, return to the relevant workshop setup or module. Each maintained workshop lists its expected inputs, checkpoints, and software support route.

Standards and Specifications

These are the canonical references for formats and data exchange used across breeding and genomic workflows.

Resource Use it for Official reference
Variant Call Format Genomic variants, genotype fields, depth, and allele counts HTS specifications and current VCF documents
Breeding API Exchanging germplasm, trial, phenotype, and genotype data between breeding applications BrAPI documentation
MIAPPE Recording the metadata needed to understand and reuse a plant phenotyping experiment MIAPPE 1.1 publication and data model
Crop Ontology Standard trait, method, and scale definitions for crop phenotyping Crop Ontology

Use the version of a standard that matches the tool and project requirements. Record that version with the analysis rather than writing only “VCF” or “BrAPI” in the methods.

Reproducibility Checklist

Before the Analysis

  • Preserve the original input files as read-only copies.
  • Record where the data came from and whether they are observed, simulated, or transformed.
  • Check sample IDs, marker IDs, ploidy, missing-value codes, reference assembly, and coordinate system.
  • Calculate a checksum for every input that will be shared or archived.
  • Define the biological question and the samples to which the result should apply.

On macOS or Linux, calculate a SHA-256 checksum with:

shasum -a 256 path/to/file

During the Analysis

  • Save consequential filtering thresholds and model settings.
  • Record retained marker and sample counts after major transformations.
  • Keep diagnostic plots and tables, not only the final figure.
  • Give outputs stable names that identify the analysis stage.
  • Record warnings and failed attempts when they affected a later decision.

When Reporting or Archiving

  • Record the software and package versions.
  • Describe the samples, trait, reference assembly, filtering, model, and validation design.
  • Include checksums and a data dictionary with shared files.
  • Separate known simulation truth from conclusions inferred by the analysis.
  • State where code, data, and restricted materials can be accessed.

For an R analysis, save the session information:

sessionInfo()
packageVersion("BIGr")

Citations and Licenses

Use the citation supplied by the software repository or installed R package. In R, check whether a package provides a citation with:

citation("packageName")

Also record the exact software version and repository URL. A paper citation identifies the method or software project; the version identifies the code that produced the result.

When reusing a figure, dataset, or other third-party asset, retain its creator, source link, and license. Confirm that the license permits the intended reuse and note whether the material was modified.

Example Data and Downloads

The BIGapp workshop dataset guide provides a fully simulated diversity panel with file definitions, direct downloads, checksums, expected record counts, and verified filtering results. It is suitable for learning and software checks, not for biological inference.

For package-specific example data, use the examples distributed with that package or linked from its software page. This keeps example files synchronized with the code that reads them.

For Contributors

Documentation authors and maintainers should use the repository’s contributor guide for content types, learning metadata, writing expectations, and listing behavior. Contributor standards remain separate from this public reference page.

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