sample-diversity

genome-sampler sample-diversity¶

Sample context sequences to a collection of divergent sequences. This is useful for retaining the diversity of the context sequences in a smaller data set, and for downsampling abundant lineages.

Citations¶

Bolyen et al., 2020; Rognes et al., 2016

Inputs¶

context_seqs: FeatureData[Sequence]

The context sequences to be sampled from.[required]

Parameters¶

percent_id: Float % Range(0, 1, inclusive_end=True)

The percent identity threshold for clustering. Context sequences will be dereplicated such that no pair of retained sequences will have a percent identity to one another that is this high.[required]

n_threads: Int % Range(1, None)

The number of threads to use for processing.[default: 1]

Outputs¶

selection: FeatureData[Selection]

The selected ids (i.e., the diversity-sampled context sequences).[required]