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

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

Usage

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

Arguments

genomeFile

Name of FASTA file holding genome sequence

runner

The job manager, specifying how the command will be run (e.g. locally, or via SLURM)

bascetInstance

A Bascet instance