bowtie_build {Rbowtie} | R Documentation

## Interface to bowtie

### Description

The following functions can be used to call the bowtie and bowtie-build binaries.

We recommend to use the QuasR package instead of using `bowtie` and `bowtie_build` directly. QuasR provides a simpler interface than Rbowtie and covers the whole analysis workflow of typical ultra-high throughput sequencing experiments, starting from the raw sequence reads, over pre-processing and alignment, up to quantification.

### Usage

    bowtie_build(references, outdir, ..., prefix = "index", force = FALSE,
    strict = TRUE)

    bowtie(sequences, index, ..., type = c("single", "paired", "crossbow"),
    outfile, force = FALSE, strict = TRUE)

    bowtie_build_usage()

    bowtie_usage()

    bowtie_version()

### Arguments

`references` | Character vector. The path to the files containing the references for which to build a bowtie index.
`outdir` | Character scalar. The path to the output directory in which to store the bowtie index. If the directory already exists, the function function will cast an error, unless `force==TRUE`.
`prefix` | Character scalar. The prefix to use for the bowtie index files.
`sequences` | If `type` is either `single` or `crossbow`, a character vector of filenames if additional argument `c==FALSE`, otherwise a vector of read sequences. If `type` is `paired`, a list of filnames ore sequences of length 2, where the first list item corresponds to the fist mate pair sequences, and the second list item to the second mate pair sequences.
`index` | Character scalar. The path to the bowtie index and prefix to align against, in the form `</path/to/index>/<prefix>`.
`type` | Character scalar, one in `c("single", "paired", "crossbow")`. If `single`, the input sequences are interpreted as single reads. If `paired`, they are supposed to be mate pair reads and if `crossbow`, they are considered to be Crossbow-style reads.
`outfile` | Character scalar. A path to a files used for the alignment output. If missing, the alignments will be returned as a regular R character vector.
`force` | Logical. Force overwriting of `outdir` or `outfile`.
`strict` | Logical. Turn off strict checking of input arguments.
`...` | Additional arguments to be passed on to the binaries. See below for details.

### Details

All additional arguments in `...` are interpreted as additional parameters to be passed on to the binaries. For flags, those are supposed to be logicals (e.g., `quiet=TRUE` will be translated into `--q`, `q=TRUE` in `-q`, and so on). Parameters with additional input are supposed to be character or numeric vectors, where the individual vector elements are collapsed into a single comma-separated string (e.g., `k=2` is translated into `k 2`, `bmax=100` into `--bmax 100`, `3=letters[1:3]` into `-3 a,b,c`, and so on). Note that some arguments to the bowtie binary will be ignored if they are already handled as explicit function arguments. See the output of `bowtie_usage()` and `bowtie_build_usage()` for details about available parameters.

### Value

The output generated by calling the binaries. For `bowtie_build` this is typically a report of the index generation, for `bowtie` this can be a vector of aligments (if `outfile` is missing), otherwise an empty character scalar.

`bowtie_usage()` and `bowtie_build_usage()` return the usage information for the respective binaries.

`bowtie_version()` return the bowtie versions information.

### Author(s)

Florian Hahne

### References

Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25.

Langmead B, Schatz M, Lin J, Pop M, Salzberg SL. Searching for SNPs with cloud computing. Genome Biology 10:R134.

### Examples

    td <- tempdir()

    ## Building a bowtie index
    refs <- dir(system.file(package="Rbowtie", "samples", "refs"),
    full=TRUE)
    tmp <- bowtie_build(references=refs, outdir=file.path(td, "index"),
    force=TRUE)
    head(tmp)
    dir(file.path(td, "index"))
    tmp2 <- bowtie_build(references=refs, outdir=file.path(td,"indexColor"),
    force=TRUE, C=TRUE)
    dir(file.path(td, "indexColor"))
    head(tmp2)

    ## Alignments
    reads <- system.file(package="Rbowtie", "samples", "reads", "reads.fastq")
    tmp <- bowtie(sequences=reads, index=file.path(td, "index", "index"))
    tmp
    bowtie(sequences=reads, index=file.path(td, "index", "index"),
    outfile=file.path(td, "alignments.txt"), best=TRUE, force=TRUE)
    readLines(file.path(td, "alignments.txt"))

    bowtie(sequences=list("TGGGTGGGGTATTCTAGAAATTTCTATTAATCCT",
                          "TCTGTTCAAGTCAGATGGTCACCAATCTGAAGAC"),
    index=file.path(td, "index", "index"), type="paired", c=TRUE)

[Package Rbowtie version 1.27.1 Index]