Docstring:
Usage: qiime feature-classifier classify-consensus-vsearch
[OPTIONS]
Assign taxonomy to query sequences using VSEARCH. Performs VSEARCH global
alignment between query and reference_reads, then assigns consensus taxonomy
to each query sequence from among maxaccepts top hits, min_consensus of
which share that taxonomic assignment. Unlike classify-consensus-blast, this
method searches the entire reference database before choosing the top N
hits, not the first N hits.
Inputs:
--i-query ARTIFACT FeatureData[Sequence]
Query Sequences. [required]
--i-reference-reads ARTIFACT FeatureData[Sequence]
Reference sequences. [required]
--i-reference-taxonomy ARTIFACT FeatureData[Taxonomy]
Reference taxonomy labels. [required]
Parameters:
--p-maxaccepts VALUE Int % Range(1, None) | Str % Choices('all')
Maximum number of hits to keep for each query. Set
to "all" to keep all hits > perc-identity
similarity. Note that if strand=both, maxaccepts
will keep N hits for each direction (if searches in
the opposite direction yield results that exceed the
minimum perc-identity). In those cases use maxhits
to control the total number of hits returned. This
option works in pair with maxrejects. The search
process sorts target sequences by decreasing number
of k-mers they have in common with the query
sequence, using that information as a proxy for
sequence similarity. After pairwise alignments, if
the first target sequence passes the acceptation
criteria, it is accepted as best hit and the search
process stops for that query. If maxaccepts is set
to a higher value, more hits are accepted. If
maxaccepts and maxrejects are both set to "all", the
complete database is searched. [default: 10]
--p-perc-identity PROPORTION Range(0.0, 1.0, inclusive_end=True)
Reject match if percent identity to query is lower.
[default: 0.8]
--p-query-cov PROPORTION Range(0.0, 1.0, inclusive_end=True)
Reject match if query alignment coverage per
high-scoring pair is lower. [default: 0.8]
--p-strand TEXT Choices('both', 'plus')
Align against reference sequences in forward
("plus") or both directions ("both").
[default: 'both']
--p-search-exact / --p-no-search-exact
Search for exact full-length matches to the query
sequences. Only 100% exact matches are reported and
this command is much faster than the default. If
True, the perc-identity, query-cov, maxaccepts, and
maxrejects settings are ignored. Note: query and
reference reads must be trimmed to the exact same
DNA locus (e.g., primer site) because only exact
matches will be reported. [default: False]
--p-top-hits-only / --p-no-top-hits-only
Only the top hits between the query and reference
sequence sets are reported. For each query, the top
hit is the one presenting the highest percentage of
identity. Multiple equally scored top hits will be
used for consensus taxonomic assignment if
maxaccepts is greater than 1. [default: False]
--p-maxhits VALUE Int % Range(1, None) | Str % Choices('all')
Maximum number of hits to show once the search is
terminated. [default: 'all']
--p-maxrejects VALUE Int % Range(1, None) | Str % Choices('all')
Maximum number of non-matching target sequences to
consider before stopping the search. This option
works in pair with maxaccepts (see maxaccepts
description for details). [default: 'all']
--p-output-no-hits / --p-no-output-no-hits
Report both matching and non-matching queries.
WARNING: always use the default setting for this
option unless if you know what you are doing! If you
set this option to False, your sequences and feature
table will need to be filtered to exclude
unclassified sequences, otherwise you may run into
errors downstream from missing feature IDs.
[default: True]
--p-weak-id PROPORTION Range(0.0, 1.0, inclusive_end=True)
Show hits with percentage of identity of at least
N, without terminating the search. A normal search
stops as soon as enough hits are found (as defined
by maxaccepts, maxrejects, and perc-identity). As
weak-id reports weak hits that are not deduced from
maxaccepts, high perc-identity values can be used,
hence preserving both speed and sensitivity.
Logically, weak-id must be smaller than the value
indicated by perc-identity, otherwise this option
will be ignored. [default: 0.0]
--p-threads NTHREADS Number of threads to use for job parallelization.
Pass 0 to use one per available CPU. [default: 1]
--p-min-consensus NUMBER Range(0.5, 1.0, inclusive_start=False,
inclusive_end=True) Minimum fraction of assignments must match top hit
to be accepted as consensus assignment.
[default: 0.51]
--p-unassignable-label TEXT
Annotation given to sequences without any hits.
[default: 'Unassigned']
Outputs:
--o-classification ARTIFACT FeatureData[Taxonomy]
Taxonomy classifications of query sequences.
[required]
--o-search-results ARTIFACT
FeatureData[BLAST6] Top hits for each query. [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).
--recycle-pool TEXT Use a cache pool for pipeline resumption. QIIME 2
will cache your results in this pool for reuse by
future invocations. These pool are retained until
deleted by the user. If not provided, QIIME 2 will
create a pool which is automatically reused by
invocations of the same action and removed if the
action is successful. Note: these pools are local to
the cache you are using.
--no-recycle Do not recycle results from a previous failed
pipeline run or save the results from this run for
future recycling.
--parallel Execute your action in parallel. This flag will use
your default parallel config.
--parallel-config FILE Execute your action in parallel using a config at
the indicated path.
--use-cache DIRECTORY Specify the cache to be used for the intermediate
work of this pipeline. 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.
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--help Show this message and exit.
Import:
from qiime2.plugins.feature_classifier.pipelines import classify_consensus_vsearch
Docstring:
VSEARCH-based consensus taxonomy classifier
Assign taxonomy to query sequences using VSEARCH. Performs VSEARCH global
alignment between query and reference_reads, then assigns consensus
taxonomy to each query sequence from among maxaccepts top hits,
min_consensus of which share that taxonomic assignment. Unlike classify-
consensus-blast, this method searches the entire reference database before
choosing the top N hits, not the first N hits.
Parameters
----------
query : FeatureData[Sequence]
Query Sequences.
reference_reads : FeatureData[Sequence]
Reference sequences.
reference_taxonomy : FeatureData[Taxonomy]
Reference taxonomy labels.
maxaccepts : Int % Range(1, None) | Str % Choices('all'), optional
Maximum number of hits to keep for each query. Set to "all" to keep all
hits > perc_identity similarity. Note that if strand=both, maxaccepts
will keep N hits for each direction (if searches in the opposite
direction yield results that exceed the minimum perc_identity). In
those cases use maxhits to control the total number of hits returned.
This option works in pair with maxrejects. The search process sorts
target sequences by decreasing number of k-mers they have in common
with the query sequence, using that information as a proxy for sequence
similarity. After pairwise alignments, if the first target sequence
passes the acceptation criteria, it is accepted as best hit and the
search process stops for that query. If maxaccepts is set to a higher
value, more hits are accepted. If maxaccepts and maxrejects are both
set to "all", the complete database is searched.
perc_identity : Float % Range(0.0, 1.0, inclusive_end=True), optional
Reject match if percent identity to query is lower.
query_cov : Float % Range(0.0, 1.0, inclusive_end=True), optional
Reject match if query alignment coverage per high-scoring pair is
lower.
strand : Str % Choices('both', 'plus'), optional
Align against reference sequences in forward ("plus") or both
directions ("both").
search_exact : Bool, optional
Search for exact full-length matches to the query sequences. Only 100%
exact matches are reported and this command is much faster than the
default. If True, the perc_identity, query_cov, maxaccepts, and
maxrejects settings are ignored. Note: query and reference reads must
be trimmed to the exact same DNA locus (e.g., primer site) because only
exact matches will be reported.
top_hits_only : Bool, optional
Only the top hits between the query and reference sequence sets are
reported. For each query, the top hit is the one presenting the highest
percentage of identity. Multiple equally scored top hits will be used
for consensus taxonomic assignment if maxaccepts is greater than 1.
maxhits : Int % Range(1, None) | Str % Choices('all'), optional
Maximum number of hits to show once the search is terminated.
maxrejects : Int % Range(1, None) | Str % Choices('all'), optional
Maximum number of non-matching target sequences to consider before
stopping the search. This option works in pair with maxaccepts (see
maxaccepts description for details).
output_no_hits : Bool, optional
Report both matching and non-matching queries. WARNING: always use the
default setting for this option unless if you know what you are doing!
If you set this option to False, your sequences and feature table will
need to be filtered to exclude unclassified sequences, otherwise you
may run into errors downstream from missing feature IDs.
weak_id : Float % Range(0.0, 1.0, inclusive_end=True), optional
Show hits with percentage of identity of at least N, without
terminating the search. A normal search stops as soon as enough hits
are found (as defined by maxaccepts, maxrejects, and perc_identity). As
weak_id reports weak hits that are not deduced from maxaccepts, high
perc_identity values can be used, hence preserving both speed and
sensitivity. Logically, weak_id must be smaller than the value
indicated by perc_identity, otherwise this option will be ignored.
threads : Threads, optional
Number of threads to use for job parallelization. Pass 0 to use one per
available CPU.
min_consensus : Float % Range(0.5, 1.0, inclusive_start=False, inclusive_end=True), optional
Minimum fraction of assignments must match top hit to be accepted as
consensus assignment.
unassignable_label : Str, optional
Annotation given to sequences without any hits.
Returns
-------
classification : FeatureData[Taxonomy]
Taxonomy classifications of query sequences.
search_results : FeatureData[BLAST6]
Top hits for each query.
