sapienns

Plugin Overview¶

A QIIME 2 plugin for interacting with data generated by the biobakery tools HUMAnN3 and MetaPhlAn3. This plugin doesn't run those tools, but allows users to load data that was generated with them for downstream analysis with QIIME 2 plugins.

version: 2026.4.0

website: https://github.com/gregcaporaso/q2-sapienns

user support:

https://forum.qiime2.org

Actions¶

Artifact Classes¶

Formats¶

sapienns metaphlan-taxon¶

Filter a MetaPhlAn3 feature table to the specified taxonomic level (or stratum).

Citations¶

Beghini et al., 2021

Inputs¶

stratified_table: MetaphlanMergedAbundanceTable

A stratified MetaPhlAn3 feature table.[required]

Parameters¶

level: Int % Range(1, None)

The level (or stratum) of the feature metadata heirarchy to select from the input table.[required]

Outputs¶

table: FeatureTable[RelativeFrequency]

Filtered table containing only features at specified level (or stratum).[required]

taxonomy: FeatureData[Taxonomy]

Taxonomic feature metadata.[required]

sapienns frequency¶

Convert relative frequencies to frequencies by multipling each value by target_freq and then rounding to whole numbers. Because rounding is taking place, the total frequency per sample may not be exactly target_freq.

Inputs¶

table: FeatureTable[RelativeFrequency]

A relative frequency feature table.[required]

Parameters¶

target_freq: Int % Range(1, None)

The target per sample total frequency.[default: 100000]

Outputs¶

output_table: FeatureTable[Frequency]

A frequency feature table.[required]

sapienns humann-pathway¶

Prepare HUMAnN3 pathway table and pathway metadata for QIIME 2. The table is prepared so that only stratified (i.e., including taxa) or unstratified (i.e., not including taxa) data are included in the output.

Citations¶

Beghini et al., 2021

Inputs¶

pathway_table: HumannPathAbundanceTable

A stratified HUMAnN3 pathway table.[required]

Parameters¶

strip_units_from_sample_ids: Bool

Remove units from input sample ids.[default: True]

destratify: Bool

Only include un-stratified pathways (i.e., those not including taxa) in the output table. By default, only stratified pathways will be included in the output table.[default: False]

Outputs¶

table: FeatureTable[Frequency]

Output feature table.[required]

taxonomy: FeatureData[Taxonomy]

Output feature metadata.[required]

sapienns humann-genefamily¶

Prepare HUMAnN3 gene family table and gene family metadata for QIIME 2. The table is prepared so that only stratified (i.e., including taxa) or unstratified (i.e., not including taxa) data are included in the output.

Citations¶

Beghini et al., 2021

Inputs¶

genefamily_table: HumannGeneFamilyTable

A stratified HUMAnN3 gene family table.[required]

Parameters¶

strip_units_from_sample_ids: Bool

Remove units from input sample ids.[default: True]

destratify: Bool

Only include un-stratified gene families (i.e., those not including taxa) in the output table. By default, only stratified pathways will be included in the output table.[default: False]

Outputs¶

table: FeatureTable[Frequency]

Output feature table.[required]

taxonomy: FeatureData[Taxonomy]

Output feature metadata.[required]