sepp: Insert fragment sequences using SEPP into reference phylogenies.¶

Docstring:

Usage: qiime fragment-insertion sepp [OPTIONS]

  Perform fragment insertion of sequences using the SEPP algorithm.

Inputs:
  --i-representative-sequences ARTIFACT FeatureData[Sequence]
                         The sequences to insert into the reference tree.
                                                                    [required]
  --i-reference-database ARTIFACT SeppReferenceDatabase
                         The reference database to insert the representative
                         sequences into.                            [required]
Parameters:
  --p-alignment-subset-size INTEGER
                         Each placement subset is further broken into subsets
                         of at most these many sequences and a separate HMM is
                         trained on each subset.               [default: 1000]
  --p-placement-subset-size INTEGER
                         The tree is divided into subsets such that each
                         subset includes at most these many subsets. The
                         placement step places the fragment on only one
                         subset, determined based on alignment scores. Further
                         reading:
                         https://github.com/smirarab/sepp/blob/master/tutorial
                         /sepp-tutorial.md#sample-datasets-default-parameters.
                                                               [default: 5000]
  --p-threads NTHREADS   The number of threads to use. Pass 0 to use one per
                         available core.                          [default: 1]
  --p-debug / --p-no-debug
                         Collect additional run information to STDOUT for
                         debugging. Temporary directories will not be removed
                         if run fails.                        [default: False]
Outputs:
  --o-tree ARTIFACT      The tree with inserted feature data.
    Phylogeny[Rooted]                                               [required]
  --o-placements ARTIFACT
    Placements           Information about the feature placements within the
                         reference tree.                            [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.
  --use-cache DIRECTORY  Specify the cache to be used for the intermediate
                         work of this action. If not provided, the default
                         cache under $TMP/qiime2/ will be used.
                         IMPORTANT FOR HPC USERS: If you are on an HPC system
                         and are using parallel execution it is important to
                         set this to a location that is globally accessible to
                         all nodes in the cluster.
  --help                 Show this message and exit.