Warning
This site has been replaced by the new QIIME 2 “amplicon distribution” documentation, as of the 2025.4 release of QIIME 2. You can still access the content from the “old docs” here for the QIIME 2 2024.10 and earlier releases, but we recommend that you transition to the new documentation at https://amplicon-docs.qiime2.org. Content on this site is no longer updated and may be out of date.
Are you looking for:
the QIIME 2 homepage? That’s https://qiime2.org.
learning resources for microbiome marker gene (i.e., amplicon) analysis? See the QIIME 2 amplicon distribution documentation.
learning resources for microbiome metagenome analysis? See the MOSHPIT documentation.
installation instructions, plugins, books, videos, workshops, or resources? See the QIIME 2 Library.
general help? See the QIIME 2 Forum.
Old content beyond this point… 👴👵
classify-otus-experimental: Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny.¶
Docstring:
Usage: qiime fragment-insertion classify-otus-experimental
[OPTIONS]
Experimental: Use the resulting tree from 'sepp' and find closest OTU-ID for
every inserted fragment. Then, look up the reference lineage string in the
reference taxonomy.
Inputs:
--i-representative-sequences ARTIFACT FeatureData[Sequence]
The sequences used for a 'sepp' run to produce the
'tree'. [required]
--i-tree ARTIFACT The tree resulting from inserting fragments into a
Phylogeny[Rooted] reference phylogeny, i.e. the output of function
'sepp' [required]
--i-reference-taxonomy ARTIFACT FeatureData[Taxonomy]
Reference taxonomic table that maps every OTU-ID
into a taxonomic lineage string. [required]
Outputs:
--o-classification ARTIFACT FeatureData[Taxonomy]
Taxonomic lineages for inserted fragments. [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.
Import:
from qiime2.plugins.fragment_insertion.methods import classify_otus_experimental
Docstring:
Experimental: Obtain taxonomic lineages, by finding closest OTU in
reference phylogeny.
Experimental: Use the resulting tree from 'sepp' and find closest OTU-ID
for every inserted fragment. Then, look up the reference lineage string in
the reference taxonomy.
Parameters
----------
representative_sequences : FeatureData[Sequence]
The sequences used for a 'sepp' run to produce the 'tree'.
tree : Phylogeny[Rooted]
The tree resulting from inserting fragments into a reference phylogeny,
i.e. the output of function 'sepp'
reference_taxonomy : FeatureData[Taxonomy]
Reference taxonomic table that maps every OTU-ID into a taxonomic
lineage string.
Returns
-------
classification : FeatureData[Taxonomy]
Taxonomic lineages for inserted fragments.