Salmon is a computational genomics tool for transcriptomic analysis. For more information, see the tool's GitHub repo. Toolchest supports running salmon quant with pre-built indexes in mapping mode.

Function Call

toolchest.salmon(
    read_one=None,
    read_two=None,
    single_end=None,
    output_path=None,
    tool_args="",
    database_name="salmon_hg38",
    database_version="1",
    library_type="A",
    is_async=False,
)
toolchest$salmon(
    read_one = NULL,
    read_two = NULL,
    single_end = NULL,
    output_path = NULL,
    tool_args = "",
    database_name = "salmon_hg38",
    database_version = "1",
    library_type = "A",
    is_async = FALSE
)

Function Arguments

ArgumentUse in place of:Description
read_one-1(optional) Path or list of paths to R1 of paired-end read input files. The files can be a local or remote, see Inputs and Outputs.
read_two-2(optional) Path or list of paths to R2 of paired-end read input files. The files can be a local or remote, see Inputs and Outputs.
single_end-r(optional) Path or list of paths to of single-end (or just R1 or R2) read input files. The files can be a local or remote, see Inputs and Outputs.
output_pathoutput file location(optional) Path (directory) to where the output files will be downloaded. If omitted, skips download. The files can be a local or remote, see Inputs and Outputs.
tool_argsall other arguments(optional) Additional arguments to be passed to Salmon. This should be a string of arguments like the command line.
database_name-i(optional) Name of database to use for Kraken 2 alignment. Defaults to "salmon_hg38".
database_version-i(optional) Version of database to use for Kraken 2 alignment. Defaults to "1".
library_type-l, --libType(optional) The library type used. Defaults to "A" for automatic classification. See the Salmon docs on library types for more.
is_asyncWhether to run a job asynchronously. See Async Runs for more.

*See the Databases section for more details.

Notes

Paired-end inputs

Paired-end read inputs can be set with either inputs or through read_one and read_two.

Make sure that the first item in read_one corresponds to the first item in read_two – and so on.

If you only have one end of a paired-end run, use the single_end argument.

Tool Versions

Toolchest currently supports version 1.9.0 of Salmon.

Databases

Toolchest currently supports the following databases for Salmon:

database_namedatabase_versionDescription
hg381hg38 precomputed index for Salmon, pulled from http://refgenomes.databio.org/.

Other modes

Only quant mode is supported at this time.


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