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bowtie2-build: Build bowtie2 index from reference sequences.

Citations

  • Ben Langmead and Steven L Salzberg. Fast gapped-read alignment with bowtie 2. Nature methods, 9(4):357, 2012.

Docstring:

Usage: qiime quality-control bowtie2-build [OPTIONS]

  Build bowtie2 index from reference sequences.

Inputs:
  --i-sequences ARTIFACT FeatureData[Sequence]
                          Reference sequences used to build bowtie2 index.
                                                                    [required]
Parameters:
  --p-n-threads NTHREADS  Number of threads to launch.            [default: 1]
Outputs:
  --o-database ARTIFACT   Bowtie2 index.
    Bowtie2Index                                                    [required]
Miscellaneous:
  --output-dir PATH       Output unspecified results to a directory
  --verbose / --quiet     Display verbose output to stdout and/or stderr
                          during execution of this action. Or silence output
                          if execution is successful (silence is golden).
  --example-data PATH     Write example data and exit.
  --citations             Show citations and exit.
  --help                  Show this message and exit.

Import:

from qiime2.plugins.quality_control.methods import bowtie2_build

Docstring:

Build bowtie2 index from reference sequences.

Build bowtie2 index from reference sequences.

Parameters
----------
sequences : FeatureData[Sequence]
    Reference sequences used to build bowtie2 index.
n_threads : Threads, optional
    Number of threads to launch.

Returns
-------
database : Bowtie2Index
    Bowtie2 index.