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Qiime

Qiime2 is an end to end microbiome analysis pipeline. Consisting of several tools that handle everything from demultiplexing to phylogenetic analysis.

Using the module​

module load biocontainers
module load qiime2

After loading the biocontainers module, you can see the available commands by running:

report_subtools.sh qiime2

Example​

For additional information and a plethora of examples see the Qiime documentation.

ml biocontainers qiime2
qiime demux emp-single \
    --i-seqs emp-single-end-sequences.qza \
    --m-barcodes-file sample_metadata.tsv \
    --m-barcodes-column barcode-sequence \
    --o-per-sample-sequences demux.qza \
    --o-error-correction-details demux-details.qza

Parallel Capabilities: Single core default, Some tools support Multithreading, please see documentation.