kraken2: Kraken 2 Client

In gotoolchest/toolchest-client-r: R Client for Toolchest

Kraken 2 Client

Description

Starts a query for Kraken 2 using Toolchest.

Usage

kraken2(
  tool_args = "",
  read_one,
  read_two = NULL,
  output_path = NULL,
  database_name = "standard",
  database_version = "1",
  ...
)

Arguments

tool_args	(optional) Additional arguments to be passed to Kraken 2.
read_one	Path of input file to be passed in as read one.
read_two	(optional) Path of input file to be passed in as read two.
output_path	(optional) Path to a directory where the output file(s) will be downloaded.
database_name	(optional) Name (string) of database to use for Kraken 2 alignment.
database_version	(optional) Version (string) of database to use for Kraken 2 alignment.
is_async	(optional) Whether to run a job asynchronously. Defaults to false.

Details

If output_path is left unspecified, downloading will be skipped.

Value

Reference to an object with output location data.

Note

If the database is unspecified, Kraken 2 will use the standard database, using index files generated by Ben Langmead's lab at https://benlangmead.github.io/aws-indexes/k2.

gotoolchest/toolchest-client-r documentation built on July 14, 2022, 7 a.m.