Detect whether a dataset is reference-guided or de novo assembled

Source: R/detect_ref_genome.R

Determine if genomic data were produced using a **reference genome** (reference-assisted assembly) or using a **de novo assembly**.

The function integrates multiple sources of evidence depending on the input provided:

1. Radiator GDS (preferred) If a radiator-generated GDS is supplied, the function checks, in order:

  • the /radiator/reference.genome node (logical value);

  • the /radiator/markers.meta/CHROM field;

  • the SeqArray chromosome node.

2. VCF imported with SeqArray or read by radiator When a VCF has been converted to GDS via SeqArray, or when a VCF file is provided directly, the function may detect reference-guided assembly from:

  • the VCF header’s ##reference= field;

  • the presence of ##contig=<ID=...> definitions;

  • the structure of chromosome labels.

3. Data-source-specific heuristics Additional rules are applied for specific pipelines:

  • Stacks: optionally, detection of . or + in annotation/id (see internal comments in the function body);

  • GATK: chromosome names containing "contig";

  • FreeBayes: inspection of reference and contig metadata in the VCF header.

detect_ref_genome(data = NULL, verbose = TRUE)

Arguments

data

A radiator GDS object, a SeqArray GDS object, or a path to a file. If provided, the function extracts information from radiator metadata, SeqArray header fields, markers.meta, and other pipeline-specific indicators. Default: data = NULL.

verbose

(logical, optional) When TRUE, the function prints messages describing the decision process and final classification. Default: verbose = TRUE.

Value

A single logical value:

  • TRUE – reference-assisted assembly;

  • FALSE – de novo assembly.

Author

Thierry Gosselin thierrygosselin@icloud.com

Examples

if (FALSE) { # \dontrun{
# Using a radiator GDS file
gds <- radiator::read_rad("my_data.gds")
ref.genome <- radiator::detect_ref_genome(data = gds)

# Using a VCF file directly
ref.genome <- radiator::detect_ref_genome(data = "variants.vcf.gz")
} # }