qiime vsearch uchime-ref (version 2019.4)

--i-sequences: ARTIFACT FeatureData[Sequence] The feature sequences to be chimera-checked. [required]:

--i-table: ARTIFACT FeatureTable[Frequency] Feature table (used for computing total feature abundances). [required]:

--i-reference-sequences: ARTIFACT FeatureData[Sequence] The non-chimeric reference sequences. [required]:

--p-dn: NUMBER No vote pseudo-count, corresponding to the Range(0.0, None) parameter n in the chimera scoring function. [default: 1.4]:

--p-mindiffs: INTEGER Minimum number of differences per segment. Range(1, None) [default: 3]:

--p-mindiv: NUMBER Minimum divergence from closest parent. Range(0.0, None) [default: 0.8]:

--p-minh: PROPORTION Range(0.0, 1.0, inclusive_end=True) Minimum score (h). Increasing this value tends to reduce the number of false positives and to decrease sensitivity. [default: 0.28]:

--p-xn: NUMBER Range(1.0, None, inclusive_start=False) No vote weight, corresponding to the parameter beta in the scoring function. [default: 8.0]:

Reference-based chimera filtering with vsearch.

Apply the vsearch uchime_ref method to identify chimeric feature sequences. The results of this method can be used to filter chimeric features from the corresponding feature table. For additional details, please refer to the vsearch documentation.

Parameters

sequences : FeatureData[Sequence]: The feature sequences to be chimera-checked.
table : FeatureTable[Frequency]: Feature table (used for computing total feature abundances).
reference_sequences : FeatureData[Sequence]: The non-chimeric reference sequences.
dn : Float % Range(0.0, None), optional: No vote pseudo-count, corresponding to the parameter n in the chimera scoring function.
mindiffs : Int % Range(1, None), optional: Minimum number of differences per segment.
mindiv : Float % Range(0.0, None), optional: Minimum divergence from closest parent.
minh : Float % Range(0.0, 1.0, inclusive_end=True), optional: Minimum score (h). Increasing this value tends to reduce the number of false positives and to decrease sensitivity.
xn : Float % Range(1.0, None, inclusive_start=False), optional: No vote weight, corresponding to the parameter beta in the scoring function.
threads : Int % Range(0, 256, inclusive_end=True), optional: The number of threads to use for computation. Passing 0 will launch one thread per CPU core.

Returns

chimeras : FeatureData[Sequence]: The chimeric sequences.
nonchimeras : FeatureData[Sequence]: The non-chimeric sequences.
stats : UchimeStats: Summary statistics from chimera checking.