bowtie2-build {Rbowtie2} | R Documentation

## Interface to bowtie2-2.4.4 build function

### Description

This function can be use to call the bowtie2-build wrapper which wraps the `bowtie2-build-s` and the `bowtie2-build-l` binaries.

### Usage

    bowtie2_build(references, bt2Index, ..., overwrite = FALSE)

### Arguments

`references` | `Character` vector. The path to the files containing the references for which to build a bowtie index.
`bt2Index` | `Character` scalar. The path where the bowtie2 index files should be created. Include the basename of the index file at the end of the path (i.e. path_to_index_dir/index_basename).
`...` | Additional arguments to be passed on to the binaries. See below for details.
`overwrite` | `Logical`. Force overwriting of existing files if setting `TRUE`.

### Details

All additional arguments in ... are interpreted as additional parameters to be passed on to bowtie2_build wrapper. All of them should be `Character` or `Numeric` scalar. You can put all additional arguments in one `Character` (e.g. "–threads 8 –quiet") with white space separation, or put them in different `Character` (e.g. "–threads","8","–quiet"). See the output of `bowtie2_build_usage()` for details about available parameters.

### Value

An invisible `Integer` of call status. The value is 0 when there is not any mistakes Otherwise the value is non-zero.

### Author(s)

Zheng Wei

### References

Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature methods, 9(4), 357-359.

### Examples

    td <- tempdir()

    ## Building a bowtie2 index

    refs <- dir(system.file(package="Rbowtie2", "extdata", "bt2","refs"),
    full=TRUE)

    bowtie2_build(references=refs, bt2Index=file.path(td, "lambda_virus"),
    "--threads 4 --quiet",overwrite=TRUE)

    ## Use additional arguments in another way

    bowtie2_build(references=refs, bt2Index=file.path(td, "lambda_virus"),
    "--threads",4,"--quiet",overwrite=TRUE)

    ## The function will print the output during the process without "--quiet" argument.
    bowtie2_build(references=refs, bt2Index=file.path(td, "lambda_virus"),
    overwrite=TRUE)

[Package Rbowtie2 version 2.0.0 Index]