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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

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

Function Arguments

Argument Use in place of: Description
inputs -U Path to one or more files to use as input. The files can be a local or remote, see Using Files.
output_path -S (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 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 Async Runs for more.

See the Databases section for more details.

Output Files

A Bowtie 2 run will output these files into output_path:

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

Notes

Paired-end inputs

Paired-end read inputs can be provided through inputs.

Tool Versions

Toolchest currently supports version 2.4.4. of Bowtie 2.

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.