qiime feature-classifier classify-consensus-vsearch (version 2019.4)

--i-query: ARTIFACT FeatureData[Sequence] Sequences to classify taxonomically. [required]:

--i-reference-reads: ARTIFACT FeatureData[Sequence] reference sequences. [required]:

--p-maxaccepts: INTEGER Maximum number of hits to keep for each query. Set Range(0, None) to 0 to keep all hits > perc-identity similarity. Must be in range [0, infinity]. [default: 10]:

--p-perc-identity: PROPORTION Range(0.0, 1.0, inclusive_end=True) Reject match if percent identity to query is lower. Must be in range [0.0, 1.0]. [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. Must be in range [0.0, 1.0]. [default: 0.8]:

--p-strand: Align against reference sequences in forward ('plus') or both directions ('both'). [default: 'both']:

--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. Must be in range (0.5, 1.0]. [default: 0.51]:

--p-unassignable-label: TEXT [default: 'Unassigned']:

VSEARCH 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]: Sequences to classify taxonomically.
reference_reads : FeatureData[Sequence]: reference sequences.
reference_taxonomy : FeatureData[Taxonomy]: reference taxonomy labels.
maxaccepts : Int % Range(0, None), optional: Maximum number of hits to keep for each query. Set to 0 to keep all hits > perc_identity similarity. Must be in range [0, infinity].
perc_identity : Float % Range(0.0, 1.0, inclusive_end=True), optional: Reject match if percent identity to query is lower. Must be in range [0.0, 1.0].
query_cov : Float % Range(0.0, 1.0, inclusive_end=True), optional: Reject match if query alignment coverage per high-scoring pair is lower. Must be in range [0.0, 1.0].
strand : Str % Choices('both', 'plus'), optional: Align against reference sequences in forward ("plus") or both directions ("both").
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. Must be in range (0.5, 1.0].
unassignable_label : Str, optional

Returns

classification : FeatureData[Taxonomy]: The resulting taxonomy classifications.