katharoseq

Katharoseq is a qiime2 plugin for analyzing samples with low biomass.

Installation

To install, download this repository and navigate to the q2_katharoseq folder and run: pip install -e .

Usage

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 \