index_genome {multicrispr} | R Documentation

## Index genome

### Description

Bowtie index genome

### Usage

    index_genome(
      bsgenome,
      indexedgenomesdir = INDEXEDGENOMESDIR,
      download = TRUE,
      overwrite = FALSE
    )

### Arguments

`bsgenome` | `BSgenome-class`
`indexedgenomesdir` | string: directory with bowtie-indexed genome
`download` | TRUE (default) or FALSE: whether to download pre-indexed version if available
`overwrite` | TRUE or FALSE (default)

### Details

Checks whether already available locally. If not, checks whether indexed version can be downloaded from our s3 storage. If not, builds the index with bowtie. This can take a few hours, but is a one-time operation.

### Value

invisible(genomdir)

### Examples

    bsgenome <- BSgenome.Scerevisiae.UCSC.sacCer1::Scerevisiae
    index_genome(bsgenome, indexedgenomesdir = tempdir())

[Package multicrispr version 1.4.3 Index]