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evaluate-seqs: Compare query (observed) vs. reference (expected) sequences.¶
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Docstring:
Usage: qiime quality-control evaluate-seqs [OPTIONS]
This action aligns a set of query (e.g., observed) sequences against a set
of reference (e.g., expected) sequences to evaluate the quality of
alignment. The intended use is to align observed sequences against expected
sequences (e.g., from a mock community) to determine the frequency of
mismatches between observed sequences and the most similar expected
sequences, e.g., as a measure of sequencing/method error. However, any
sequences may be provided as input to generate a report on pairwise
alignment quality against a set of reference sequences.
Inputs:
--i-query-sequences ARTIFACT FeatureData[Sequence]
Sequences to test for exclusion [required]
--i-reference-sequences ARTIFACT FeatureData[Sequence]
Reference sequences to align against feature
sequences [required]
Parameters:
--p-show-alignments / --p-no-show-alignments
Option to plot pairwise alignments of query
sequences and their top hits. [default: False]
Outputs:
--o-visualization VISUALIZATION
[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.quality_control.visualizers import evaluate_seqs
Docstring:
Compare query (observed) vs. reference (expected) sequences.
This action aligns a set of query (e.g., observed) sequences against a set
of reference (e.g., expected) sequences to evaluate the quality of
alignment. The intended use is to align observed sequences against expected
sequences (e.g., from a mock community) to determine the frequency of
mismatches between observed sequences and the most similar expected
sequences, e.g., as a measure of sequencing/method error. However, any
sequences may be provided as input to generate a report on pairwise
alignment quality against a set of reference sequences.
Parameters
----------
query_sequences : FeatureData[Sequence]
Sequences to test for exclusion
reference_sequences : FeatureData[Sequence]
Reference sequences to align against feature sequences
show_alignments : Bool, optional
Option to plot pairwise alignments of query sequences and their top
hits.
Returns
-------
visualization : Visualization