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

Function Call

tc.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,
)

Function Arguments

Argument	Use 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 Using Files.
`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 Using Files.
`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 Using Files.
`output_path`	output 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 Using Files.
`tool_args`	all 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_async`		Whether 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_name`	`database_version`	Description
`hg38`	`1`	hg38 precomputed index for Salmon, pulled from http://refgenomes.databio.org/.

Other modes

Only quant mode is supported at this time.