hisat2 {Rhisat2} | R Documentation

## Align reads with HISAT2

### Description

The function can be used to call the `hisat2` binary.

### Usage

    hisat2(
      sequences,
      index,
      ...,
      type = c("single", "paired"),
      outfile,
      force = FALSE,
      strict = TRUE,
      execute = TRUE
    )

### Arguments

`sequences` | If `type` is `single`, a character vector of file names if the additional argument `c` is FALSE, otherwise a vector of read sequences. If `type` is `paired`, a length-2 list of file names or sequences, where the first list item corresponds to the first mate pair sequences, and the second list item to the second mate pair sequences.
`index` | Character scalar. The path+prefix of the HISAT2 index to align against (in the form `<path/to/index>/<prefix>`).
`...` | Additional arguments passed to the binaries.
`type` | Character scalar, either "single" or "paired". If `single`, the input sequences are interpreted as single-end reads. If `paired`, they are supposed to be paired reads.
`outfile` | (optional) Character scalar. The path to the output file. If missing, the alignments will be returned as an R character vector.
`force` | Logical scalar. Whether to force overwriting of `outdir`.
`strict` | Logical scalar. Whether strict checking of input arguments should be enforced.
`execute` | Logical scalar. Whether to execute the assembled shell command. If FALSE, return a string with the command.

### Details

All additional arguments in `...` are interpreted as additional arguments to the HISAT2 binaries. Any flags are supposed to be represented as logical values (e.g., `quiet=TRUE` will be translated into `--quiet`). Parameters with additional input are supposed to be character or numeric vectors, and the individual elements are collapsed into a single comma-separated string (e.g., `k=2` is translated into `-k 2`, `bmax=100` into `--bmax 100`). Some arguments to the HISAT2 binaries will be ignored if they are already handled as explicit function arguments. See the output of `hisat2_usage()` for details about available parameters.

### Value

If `execute` is TRUE, the output generated by calling the `hisat2` binary. If `execute` is FALSE, the `hisat2` command.

### Author(s)

Charlotte Soneson, based on code from Florian Hahne.

### References

Kim D, Langmead B and Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nature Methods 12:357-360 (2015).

### Examples

    tmp <- tempdir()
    refs <- list.files(system.file("extdata/refs", package="Rhisat2"),
                       full.names=TRUE, pattern="\\.fa$")
    hisat2_build(references=refs, outdir=file.path(tmp, "index"),
                 force=TRUE, prefix="index")
    reads <- list.files(system.file("extdata/reads", package="Rhisat2"),
                        full.names=TRUE, pattern="\\.fastq$")
    hisat2(sequences=as.list(reads), index=file.path(tmp, "index/index"),
           type="paired", outfile=file.path(tmp, "out.sam"), force=TRUE)

[Package Rhisat2 version 1.8.0 Index]