Plugins

Convert an artifact with a registered QIIME 2 metadata transformer into metadata for downstream actions.

Perform de novo multiple sequence alignment using MAFFT.

Add new sequences to an existing alignment with MAFFT.

Mask (i.e., filter) unconserved and highly gapped columns from an alignment. Default min_conservation was chosen to reproduce the mask presented in Lane (1991).

Trim an existing alignment based on provided primers or specific, pre-defined positions. Primers take precedence over the positions,i.e. if both are provided, positions will be ignored.When using primers in combination with a DNA alignment, a new alignment will be generated to locate primer positions. Subsequently, start (5'-most) and end (3'-most) position from fwd and rev primer located within the new alignment is identified and used for slicing the original alignment. The retention of alignment positions that span the primer locations can be toggled. WARNING: finding alignment positions via primer search can be inefficient for very large alignments and is only recommended for small alignments. For large alignments providing specific alignment positions is ideal.

Given a single feature table as input, this action resamples the feature table `n` times to a total frequency of `sampling depth` per sample, and then computes the specified alpha diversity metric on each resulting `table`. The resulting artifacts are then averaged using the method specified by `average_method`, and the resulting average per-sample alpha diversities are returned.

Compute the per-sample average across a collection of alpha diversity vectors computed from the same samples.

Given a single feature table as input, this action resamples the feature table `n` times to a total frequency of `sampling depth` per sample, and then computes the specified alpha diversity metric on each resulting `table`. The resulting artifacts can be used, for example, to explore the variance across `n` iterations of resampling.