Nephele Tutorials

Importing Nephele outputs into MicrobiomeDB

MicrobiomeDB is a data-mining platform for interrogating microbiome experiments, and is part of the VEuPathDB family of NIAID Bioinformatics Resource Centers. You can explore their curated database of microbiome datasets, and if you create an account, you can also upload your own biom file for visualization, analysis and comparison with MicrobiomeDB's studies - see the MicrobiomeDB FAQ.

Once you have a MicrobiomeDB account, you can directly transfer your Nephele results to your MicrobiomeDB workspace using the "Analyze results with MicrobiomeDB" link on the pipeline results page for your completed job. Alternately, you can upload the Nephele biom file yourself through the My Data Sets form on MicrobiomeDB.

The following Nephele pipeline biom files have the necessary metadata to be compatible with MicrobiomeDB's analysis tools:

  • DADA2/DADA2 ITS: taxa.biom which is the final output of the taxonomic classification step of the pipeline.
  • mothur: combo.trim.contigs.good.unique.good.filter.unique.precluster.pick.opti_mcc.0.03.biom
  • Whole metagenome sequence assembly (wgsa): all_samples_mapped_reads.biom
  • Downstream analysis: input_with_annotations.biom which is the input biom file that you submit to the pipeline with the metadata from your mapping file added. If you have a biom file for which you wish to add or edit the metadata, you can submit it first to this pipeline. For example, if your biom file for a completed Nephele job from a different analysis pipeline is missing some metadata, rather than re-run the sequence analysis, you can edit the mapping file to add those columns, and then submit it along with the biom file to the Downstream analysis pipeline. This with produce the biom file with the desired metadata, and save time as this pipeline can be much faster to run.

For best comparison of your data with the MicrobiomeDB 16S datasets, we recommend using Nephele's DADA2 pipeline with the SILVA taxonomic database, as these are the tools MicrobiomeDB has used for sequence analysis.

Examples of MicrobiomeDB analyses

Screenshot of MicrobiomeDB differential abundance
Screenshot of MicrobiomeDB differential abundance