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]