Index a genome using Bowtie2 such that it can be used for alignment

Usage

BascetIndexGenomeBowtie2(
  genomeFile,
  numThreads = NULL,
  overwrite = FALSE,
  runner = GetDefaultBascetRunner(),
  bascetInstance = GetDefaultBascetInstance()
)

Arguments

genomeFile: Name of FASTA file holding genome sequence
numThreads: Number of threads to use. Default is the maximum, taken from runner settings
overwrite: Force overwriting of existing files. The default is to do nothing if files exist
runner: The job manager, specifying how the command will be run (e.g. locally, or via SLURM)
bascetInstance: A Bascet instance