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classify-consensus-vsearch: VSEARCH-based consensus taxonomy classifier¶
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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. --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.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.