Nephele Tutorials

Importing Nephele outputs into QIIME 2

Nephele uses various plugins from QIIME 2 for our pipelines, but you may also want to do your own analysis using QIIME 2. This tutorial is using QIIME 2 v2019.7. It assumes you have already installed QIIME 2 and have activated the conda environment.

DADA2 pipeline

  • Import ASV count data from BIOM file.

    qiime tools import --type FeatureTable[Frequency] --input-path \
    taxa_species.biom --output-path frequency_table.qza --input-format BIOMV100Format
  • Import taxonomy from taxonomy table.

    qiime tools import --type FeatureData[Taxonomy] --input-path \
    taxonomy_table.txt --output-path taxonomy_table.qza  --input-format TSVTaxonomyFormat

mothur pipeline

  • Import OTU count data from BIOM file.

    qiime tools import --type FeatureTable[Frequency] --input-path \
    combo.trim.contigs.good.unique.good.filter.unique.precluster.pick.opti_mcc.0.03.biom \
    --output-path frequency_table.qza --input-format BIOMV100Format
  • For the taxonomy, you will first need to modify the combo.trim.contigs.good.unique.good.filter.unique.precluster.pick.opti_mcc.0.03.cons.taxonomy file as follows:

    • Remove the second column "Size."
    • Rename the remaining columns to "Feature ID" and "Taxon."

    Then you can import the taxonomy from this modified file.

    qiime tools import --type FeatureData[Taxonomy] --input-path \
    modified.taxonomy --output-path taxonomy_table.qza --input-format TSVTaxonomyFormat

Downstream analysis pipeline

  • The outputs of the downstream analysis pipeline with extension .qza are already in QIIME 2 artifact format. See the QIIME 2 plugin help linked from the pipeline output files section for their artifact types.