q2-shogun

• A plugin wrapper of SHOGUN for shallow shotgun sequence profiling.

Example Usage

Test files are contained in the q2-shogun repo, so first we will clone the repo to get those files.

git clone https://github.com/qiime2/q2-shogun.git
cd q2-shogun

Taxonomic profiling

Taxonomic profiling is available via the nobunaga action, which performs alignment against a reference database, followed by LCA consensus assignment to resolve most likely taxonomic lineage. This method requires (1) query sequences as FeatureData[Sequence] (fasta format); (2) reference sequences in FeatureData[Sequence] (fasta format); (3) the taxonomic affiliations of each reference sequence; and (4) the a bowtie2 alignment index of the same reference sequences.

$ qiime shogun nobunaga --help
Usage: qiime shogun nobunaga [OPTIONS]

  Profile query sequences taxonomically via alignment with bowtie2, followed
  by LCA taxonomy assignment.

Options:
  --i-query ARTIFACT PATH FeatureData[Sequence]
                                  query sequences.  [required]
  --i-reference-reads ARTIFACT PATH FeatureData[Sequence]
                                  reference sequences.  [required]
  --i-reference-taxonomy ARTIFACT PATH FeatureData[Taxonomy]
                                  reference taxonomy labels.  [required]
  --i-database ARTIFACT PATH Bowtie2Index
                                  bowtie2 index artifact.  [required]
  --p-taxacut FLOAT               Minimum fraction of assignments must match
                                  top hit to be accepted as consensus
                                  assignment. Must be in range (0.0, 1.0].
                                  [default: 0.8]
  --p-threads INTEGER RANGE       Number of threads to use.  [default: 1]
  --p-percent-id FLOAT            Reject match if percent identity to query is
                                  lower. Must be in range [0.0, 1.0].
                                  [default: 0.98]
  --o-taxa-table ARTIFACT PATH FeatureTable[Frequency]
                                  Frequency table of taxonomic composition.
                                  [required if not passing --output-dir]
  --output-dir DIRECTORY          Output unspecified results to a directory
  --cmd-config FILE               Use config file for command options
  --verbose                       Display verbose output to stdout and/or
                                  stderr during execution of this action.
                                  [default: False]
  --quiet                         Silence output if execution is successful
                                  (silence is golden).  [default: False]
  --citations                     Show citations and exit.
  --help                          Show this message and exit.

This command will generate a feature table containing taxa observed in each sample.

qiime shogun nobunaga \
    --i-query q2_shogun/tests/data/query.qza \
    --i-reference-reads q2_shogun/tests/data/refseqs.qza \
    --i-reference-taxonomy q2_shogun/tests/data/taxonomy.qza \
    --i-database q2_shogun/tests/data/bt2-database.qza \
    --o-taxa-table taxatable.qza

Now we can use this feature table for any number of QIIME 2 actions. For example, we can make a heatmap displaying the abundance of each taxon in each sample:

qiime feature-table heatmap \
    --i-table taxatable.qza \
    --o-visualization taxatable.qzv

Importing a bowtie2 database

A bowtie2 index is generated externally using the bowtie2-build command (see the bowtie manual for more details). This will generate six files (where basename is a name defined by the user):

basename.1.bt2
basename.2.bt2
basename.3.bt2
basename.4.bt2
basename.rev.1.bt2
basename.rev.2.bt2

Put these files into a single directory that does not contain any other files; then import that directory using QIIME 2. For example, if these files are in the bowtie-db directory, we would use the following command to import our database into a single artifact:

qiime tools import --input-path bowtie-db/ --output-path bt2-database.qza --type Bowtie2Index