Docstring:
Usage: qiime vsearch dereplicate-sequences [OPTIONS]
Dereplicate sequence data and create a feature table and feature
representative sequences. Feature identifiers in the resulting artifacts
will be the sha1 hash of the sequence defining each feature. If clustering
of features into OTUs is desired, the resulting artifacts can be passed to
the cluster_features_* methods in this plugin.
Inputs:
--i-sequences ARTIFACT SampleData[Sequences] |
SampleData[SequencesWithQuality] | SampleData[JoinedSequencesWithQuality]
The sequences to be dereplicated. [required]
Parameters:
--p-derep-prefix / --p-no-derep-prefix
Merge sequences with identical prefixes. If a
sequence is identical to the prefix of two or more
longer sequences, it is clustered with the shortest
of them. If they are equally long, it is clustered
with the most abundant. [default: False]
--p-min-seq-length INTEGER
Range(1, None) Discard sequences shorter than this integer.
[default: 1]
--p-min-unique-size INTEGER
Range(1, None) Discard sequences with a post-dereplication
abundance value smaller than integer. [default: 1]
Outputs:
--o-dereplicated-table ARTIFACT FeatureTable[Frequency]
The table of dereplicated sequences. [required]
--o-dereplicated-sequences ARTIFACT FeatureData[Sequence]
The dereplicated sequences. [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.vsearch.methods import dereplicate_sequences
Docstring:
Dereplicate sequences.
Dereplicate sequence data and create a feature table and feature
representative sequences. Feature identifiers in the resulting artifacts
will be the sha1 hash of the sequence defining each feature. If clustering
of features into OTUs is desired, the resulting artifacts can be passed to
the cluster_features_* methods in this plugin.
Parameters
----------
sequences : SampleData[Sequences] | SampleData[SequencesWithQuality] | SampleData[JoinedSequencesWithQuality]
The sequences to be dereplicated.
derep_prefix : Bool, optional
Merge sequences with identical prefixes. If a sequence is identical to
the prefix of two or more longer sequences, it is clustered with the
shortest of them. If they are equally long, it is clustered with the
most abundant.
min_seq_length : Int % Range(1, None), optional
Discard sequences shorter than this integer.
min_unique_size : Int % Range(1, None), optional
Discard sequences with a post-dereplication abundance value smaller
than integer.
Returns
-------
dereplicated_table : FeatureTable[Frequency]
The table of dereplicated sequences.
dereplicated_sequences : FeatureData[Sequence]
The dereplicated sequences.
