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evaluate-seqs: Compare query (observed) vs. reference (expected) sequences.ΒΆ

Citations

[quality-control:evaluate-seqs:CCA+09]Christiam Camacho, George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer, and Thomas L Madden. Blast+: architecture and applications. BMC bioinformatics, 10(1):421, 2009. doi:10.1186/1471-2105-10-421.

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.

Options:
  --i-query-sequences ARTIFACT PATH FeatureData[Sequence]
                                  Sequences to test for exclusion  [required]
  --i-reference-sequences ARTIFACT PATH FeatureData[Sequence]
                                  Reference sequences to align against feature
                                  sequences  [required]
  --p-show-alignments / --p-no-show-alignments
                                  Option to plot pairwise alignments of query
                                  sequences and their top hits.  [default:
                                  False]
  --o-visualization VISUALIZATION PATH
                                  [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.

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