Bowtie 2 is a fast and efficient aligner for aligning reads to reference sequences, particularly for input reads of 50-1000 characters and relatively long (e.g. mammalian) reference genomes. For more information, see the tool's Sourceforge page and GitHub repo.

Function Call

toolchest.bowtie2(
    inputs,
    output_path=None,
    tool_args="",
    database_name="standard",
    database_version="1",
    is_async=False,
)

toolchest$bowtie2(
    inputs,
    output_path = NULL,
    tool_args = "",
    database_name = "standard",
    database_version = "1",
    is_async = FALSE
)

Function Arguments

Argument	Use in place of:	Description
`inputs`	`-U`	Path or list of paths (client-side) to be passed in as input(s).
`output_path`	`-S`	(optional) Path to a directory where the output files will be downloaded. This can be a local filepath or an AWS S3 URI. If omitted, skips download. The outputs can be downloaded manually.
`tool_args`	all other arguments	(optional) Additional arguments to be passed to Bowtie 2. This should be a string of arguments like the command line. See Supported Additional Arguments for more details.
`database_name`	`-x`*	(optional) Name of database to use for Bowtie 2 alignment. Defaults to `"GRCh38_noalt_as"` (human genome).
`database_version`	`-x`*	(optional) Version of database to use for Bowtie 2 alignment. Defaults to `"1"`.
`is_async`		Whether to run a job asynchronously.

*See the Databases section for more details.

Output Files

A Bowtie 2 run will output these files into the directory specified by output_path:

bowtie2.log: Log outputted to stderr.
bowtie2_output.sam: SAM file outputted by Bowtie 2.

Return Value

This function call returns a Toolchest output object, which contains the run ID and locations of downloaded output files. See Output Objects for more details.

Notes

Amazon AWS S3 inputs

Publicly available files stored on AWS's S3 service can be passed in as inputs, using the file's S3 URI.

Async runs

Set the is_async parameter to true if you would like to run a Bowtie 2 job asynchronously. See Async Runs for more information.

Paired-end inputs

Paired-end read inputs can be provided through inputs.

Tool Versions

Toolchest currently supports version 2.4.4. of Bowtie 2. Every request to run Bowtie 2 with Toolchest will default to this version.

Databases

Toolchest currently supports the following databases for Bowtie 2:

`database_name`	`database_version`	Description
`Ash1_v2.0`	`1`	Human / Ash2.0, JHU source¹
`GRCh38_noalt_as`	`1`	Human / GRCh38 no-alt analysis set, NCBI source¹
`GRCm39`	`1`	Mouse / GRCm39, NCBI source¹

¹These database indexes were generated by the Langmead Lab at Johns Hopkins and can be found on the lab's database index page.

Supported Additional Arguments

-3
-5
-a
--align-paired-reads
-D
--dovetail
--dpad
--end-to-end
-f
-F
--fast
--fast-local
--ff
--fr
--gbar
-i
-I
--ignore-quals
--int-quals
-k
-L
--local
--ma
--maxins
--minins
--mp
-N
--n-ceil
--no-1mm-upfront
--no-contain
--no-discordant
--nofw
--no-hd
--no-mixed
--non-deterministic
--no-overlap
--norc
--no-sq
--no-unal
--np
--omit-sec-seq
--phred33
--phred64
--preserve-tags
-q
--qc-filter
--qseq
-r
-R
--rdg
--rf
--rfg
--rg
--rg-id
-s
--sam-append-comment
--sam-no-qname-trunc
--score-min
--seed
--sensitive
--sensitive-local
--soft-clipped-unmapped-tlen
--solexa-quals
-t
--tab5
--tab6
--time
--trim-to
-u
--very-fast
--very-fast-local
--very-sensitive
--very-sensitive-local
-X
--xeq

Additional arguments can be specified under the tool_args argument.