```
cellranger mkref -h
```
Prepare a reference for use with 10x analysis software. Requires a GTF and
FASTA

Usage: cellranger mkref [OPTIONS] --genome <GENOME_NAMES> --fasta <FASTA_FILES> --genes <GTF_FILES>

Options:
      --genome <GENOME_NAMES>
          Unique genome name, used to name output folder [a-zA-Z0-9_-]+.
          Specify multiple genomes by specifying this argument multiple
          times; the output folder will be <name1>_and_<name2>
      --fasta <FASTA_FILES>
          Path to FASTA file containing your genome reference. Specify
          multiple genomes by specifying this argument multiple times
      --genes <GTF_FILES>
          Path to genes GTF file containing annotated genes for your genome
          reference. Specify multiple genomes by specifying this argument
          multiple times
      --nthreads <NUM_THREADS>
          Number of threads used during STAR genome index generation.
          Defaults to 1 [default: 1]
      --memgb <MEM_GB>
          Maximum memory (GB) used [default: 16]
      --ref-version <REF_VERSION>
          Optional reference version string to include with reference
      --dry
          Do not execute the pipeline. Generate a pipeline invocation (.mro)
          file and stop
      --jobmode <MODE>
          Job manager to use. Valid options: local (default), sge, lsf,
          slurm or path to a .template file. Search for help on "Cluster
          Mode" at support.10xgenomics.com for more details on configuring
          the pipeline to use a compute cluster
      --localcores <NUM>
          Set max cores the pipeline may request at one time. Only applies
          to local jobs
      --localmem <NUM>
          Set max GB the pipeline may request at one time. Only applies to
          local jobs
      --localvmem <NUM>
          Set max virtual address space in GB for the pipeline. Only applies
          to local jobs
      --mempercore <NUM>
          Reserve enough threads for each job to ensure enough memory will
          be available, assuming each core on your cluster has at least this
          much memory available. Only applies to cluster jobmodes
      --maxjobs <NUM>
          Set max jobs submitted to cluster at one time. Only applies to
          cluster jobmodes
      --jobinterval <NUM>
          Set delay between submitting jobs to cluster, in ms. Only applies
          to cluster jobmodes
      --overrides <PATH>
          The path to a JSON file that specifies stage-level overrides for
          cores and memory. Finer-grained than --localcores, --mempercore
          and --localmem. Consult https://support.10xgenomics.com/ for an
          example override file
      --output-dir <PATH>
          Output the results to this directory
      --uiport <PORT>
          Serve web UI at http://localhost:PORT
      --disable-ui
          Do not serve the web UI
      --noexit
          Keep web UI running after pipestance completes or fails
      --nopreflight
          Skip preflight checks
  -h, --help
          Print help
