run_busco: Run BUSCO assessment of assembly and annotation quality

In almeidasilvaf/cogeqc: Systematic quality checks on comparative genomics analyses

Run BUSCO assessment of assembly and annotation quality

Description

Run BUSCO assessment of assembly and annotation quality

Usage

run_busco(
  sequence = NULL,
  outlabel = NULL,
  mode = c("genome", "transcriptome", "proteins"),
  lineage = NULL,
  auto_lineage = NULL,
  force = FALSE,
  threads = 1,
  outpath = NULL,
  download_path = tempdir()
)

Arguments

sequence	An object of class DNAStringSet/AAStringSet/RNAStringSet or path to FASTA file with the genome, transcriptome, or protein sequences to be analyzed. If there are many FASTA files in a directory, you can input the path to this directory, so BUSCO will be run in all FASTA files inside it.
outlabel	Character with a recognizable short label for analysis directory and files.
mode	Character with BUSCO mode. One of 'genome', 'transcriptome', or 'proteins'.
lineage	Character with name of lineage to be used.
auto_lineage	Character indicating whether BUSCO should determine optimum lineage path automatically. One of 'euk', 'prok', 'all', or NULL. If 'euk', it will determine optimum lineage path on eukaryote tree. If 'prok', it will determine optimum lineage path on non-eukaryote trees. If 'all', it will determine optimum lineage path for all trees. If NULL, it will not automatically determine lineage, and lineage must be manually specified. Default: NULL.
force	Logical indicating whether existing runs with the same file names should be overwritten. Default: FALSE.
threads	Numeric with the number of threads/cores to use. Default: 1.
outpath	Path to results directory. If NULL, results will be stored in the current working directory. Default: NULL.
download_path	Path to directory where BUSCO datasets will be stored after downloading. Default: tempdir().

Value

A character vector with the names of subdirectories and files in the results directory.

Examples

sequence <- system.file("extdata", "Hse_subset.fa", package = "cogeqc")
download_path <- paste0(tempdir(), "/datasets")
if(busco_is_installed()) {
    run_busco(sequence, outlabel = "Hse", mode = "genome",
              lineage = "burkholderiales_odb10",
              outpath = tempdir(), download_path = download_path)
}

almeidasilvaf/cogeqc documentation built on Jan. 29, 2024, 7:20 a.m.