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Path to one of the example genomes

Source: R/tantale_data.R
tantale_genome.Rd

The articles and examples use four Xanthomonas oryzae pv. oryzae genome assemblies. They are not part of the package itself: tantale_setup() downloads them, with the Java tools, when called with install = TRUE. This function returns where one of them is.

Usage

tantale_genome(strain = c("MAI1", "BAI3", "BAI3-1-1", "PXO86"))

Arguments

strain

Which genome.

Value

The path of a FASTA file.

Details

MAI1 (GenBank CP025609.1), BAI3 (CP025610.1) and PXO86 (RefSeq NZ_CP007166.1) are complete genomes of African and Asian strains; the sequences are those of the records, with shortened FASTA headers. BAI3-1-1 is an unpublished assembly of a BAI3 derivative that carries sequencing and assembly errors in its TALE loci. It was produced by the authors of tantale, is available only from the package's genomes-1 release, and serves to illustrate frameshift correction.

See also

tantale_setup(), which downloads them.

Examples

# \donttest{
# Needs the genomes downloaded by tantale_setup(install = TRUE).
tantale_genome("MAI1")
#> [1] "/home/cunnac/snap/codium/495/.local/share/R/tantale/genomes-1/MAI1.fa"
# }