qiime feature-classifier classify-consensus-blast (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. Must Range(1, None) be in range [1, infinity]. BLAST will choose the first N hits in the reference database that exceed perc-identity similarity to query. [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. Note: this uses blastn's qcov_hsp_perc parameter, and may not behave identically to the query-cov parameter used by classify-consensus-vsearch. Must be in range [0.0, 1.0]. [default: 0.8]:

--p-strand: :

--p-evalue: NUMBER BLAST expectation value (E) threshold for saving hits. [default: 0.001]:

--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']:

BLAST+ consensus taxonomy classifier

Assign taxonomy to query sequences using BLAST+. Performs BLAST+ local alignment between query and reference_reads, then assigns consensus taxonomy to each query sequence from among maxaccepts hits, min_consensus of which share that taxonomic assignment. Note that maxaccepts selects the first N hits with > perc_identity similarity to query, not the top N matches. For top N hits, use classify-consensus-vsearch.

Parameters

query : FeatureData[Sequence]: Sequences to classify taxonomically.
reference_reads : FeatureData[Sequence]: reference sequences.
reference_taxonomy : FeatureData[Taxonomy]: reference taxonomy labels.
maxaccepts : Int % Range(1, None), optional: Maximum number of hits to keep for each query. Must be in range [1, infinity]. BLAST will choose the first N hits in the reference database that exceed perc_identity similarity to query.
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. Note: this uses blastn's qcov_hsp_perc parameter, and may not behave identically to the query_cov parameter used by classify- consensus-vsearch. Must be in range [0.0, 1.0].
strand : Str % Choices('both', 'plus', 'minus'), optional: Align against reference sequences in forward ("plus"), reverse ("minus"), or both directions ("both").
evalue : Float, optional: BLAST expectation value (E) threshold for saving hits.
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]: Taxonomy classifications of query sequences.