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vsearch-global: VSEARCH global alignment search¶
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Docstring:
Usage: qiime feature-classifier vsearch-global [OPTIONS] Search for top hits in a reference database via global alignment between the query sequences and reference database sequences using VSEARCH. Returns a report of the top M hits for each query (where M=maxaccepts or maxhits). Inputs: --i-query ARTIFACT FeatureData[Sequence] Query Sequences. [required] --i-reference-reads ARTIFACT FeatureData[Sequence] Reference sequences. [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] Outputs: --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). --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.methods import vsearch_global
Docstring:
VSEARCH global alignment search Search for top hits in a reference database via global alignment between the query sequences and reference database sequences using VSEARCH. Returns a report of the top M hits for each query (where M=maxaccepts or maxhits). Parameters ---------- query : FeatureData[Sequence] Query Sequences. reference_reads : FeatureData[Sequence] Reference sequences. 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. Returns ------- search_results : FeatureData[BLAST6] Top hits for each query.