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Merge pull request #2 from biocore/things
versioneer, documentation things, etc
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q2_katharoseq/_version.py export-subst |
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include versioneer.py | ||
include q2_katharoseq/_version.py |
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# katharoseq | ||
![](https://github.com/qiime2/q2templates/workflows/ci/badge.svg) | ||
# KatharoSeq | ||
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Katharoseq is a qiime2 plugin for analyzing samples with low biomass. | ||
An implementation of the KatharoSeq protocol, originally defined in [Minich et al 2018 mSystems](https://journals.asm.org/doi/10.1128/mSystems.00218-17). | ||
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## Installation | ||
To install, download this repository and navigate to the `q2_katharoseq` folder and run: | ||
pip install -e . | ||
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## Usage | ||
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qiime katharoseq read-count-threshold \ | ||
--p-threshold 50 \ | ||
--i-table table.qza \ | ||
--m-positive-control-column-column p_control \ | ||
--m-positive-control-column-file metadata.tsv \ | ||
--p-positive-control-value katharoseq_control \ | ||
--p-control classic \ | ||
--m-cell-count-column-column max_cell_count \ | ||
--m-cell-count-column-file metadata.tsv \ | ||
--o-visualization visualization.qzv \ | ||
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Installation assumes a working QIIME 2 environment with a minimum version of 2021.8. Details on installing QIIME 2 can be found [here](https://docs.qiime2.org/2021.11/install/). | ||
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``` | ||
git clone https://github.com/biocore/q2-katharoseq.git | ||
cd q2-katharoseq | ||
pip install -e . | ||
``` | ||
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## Use | ||
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Computation of a minimum read count threshold can be performed with the | ||
`read_count_threshold` plugin action. Computation assumes that the user has | ||
classified their 16S features against SILVA, and that the | ||
`FeatureTable[Frequency]` has been collapsed to the genus level. Please see the | ||
[`q2-feature-classifier`](https://docs.qiime2.org/2021.11/plugins/available/feature-classifier/classify-sklearn) for detail on how to perform taxonomy | ||
classification, and the [`q2-taxa`](https://docs.qiime2.org/2021.11/plugins/available/taxa/collapse) plugin for information on collapsing to a taxonomic level. | ||
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``` | ||
qiime katharoseq read_count_threshold \ | ||
--i-table a_genus_level_table.qza \ | ||
--p-control classic \ | ||
--p-positive-control-value name_of_controls_in_metadata \ | ||
--m-positive-control-column-file your_metadata.tsv \ | ||
--m-positive-control-column-column sample_type_variable_in_metadata \ | ||
--m-cell-count-column-file your_metadata.tsv \ | ||
--m-cell-count-column-column cell_count_variable_in_metadata \ | ||
--o-visualization result.qzv | ||
``` | ||
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