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

QIIME 1 pipeline

  • Import OTU count data from BIOM file. Here, we are using otus/otu_table_mc2_w_tax_no_pynast_failures.biom which is the final output of the 16S open reference OTU picking step in QIIME 1. For 16S closed or de novo OTU picking, you may want to use otus/otu_table.biom, and for ITS, otus/otu_table_mc2_w_tax.biom.

    qiime tools import --type FeatureTable[Frequency] --input-path \
    otus/otu_table_mc2_w_tax_no_pynast_failures.biom --output-path frequency_table.qza \
    --input-format BIOMV210Format
  • Import taxonomy from BIOM file.

    qiime tools import --type FeatureData[Taxonomy] --input-path \
    otus/otu_table_mc2_w_tax_no_pynast_failures.biom --output-path taxonomy_table.qza \
    --input-format BIOMV210Format

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.