How to participate in the Challenge

There are 4 ways to participate in the Standards Challenge:

  1. Be a challenge observer
  2. Sequence the samples provided by the Challenge and upload your data (link to sample descriptions)
  3. Download and analyze data and metadata submitted by other users
  4. Create and submit Mosaic Apps to analyze submitted sequencing data to study the variability stemming from bioinformatics pipelines

A Mosaic account is required to join the Challenge and participate in any of the four ways listed above. If you don’t have an account yet, you can register for free here: https://platform.mosaicbiome.com/login.

For groups interested in participating by sequencing:

  1. Request sample kit containing a set of the 7 sample aliquots. If you plan to process the samples within 2 months of receiving them, samples can be stored at room temperature, otherwise store at -20°C or -80°C.
  2. Process and sequence these samples using your own protocols.
    1. To begin processing the stool samples, simply vortex and then pipette a volume of sample compatible with your extraction method directly into the lysis tube: 250 µl of stabilized sample works well with most commercial kits and corresponds to approximately 25 mg feces (each 1 mL aliquot contains approximately 100 mg of stool sample).
    2. For optimal results, do not exceed the maximum recommended input for your extraction method. Do not decant or remove the OMNIgene•GUT Solution. Contact DNA Genotek if you have any questions: support@dnagenotek.com.
  3. Submit the protocol metadata using a controlled vocabulary to ensure consistency. We recognize that some steps in the protocol could be proprietary, so participants are encouraged to provide as much information as they can share.
  4. Upload raw sequencing data to Mosaic.
    1. Raw reads will be processed using standardized pipelines depending on the type of sequencing (16S/shotgun/others) to produce taxonomic readouts.
    2. Currently only 16S/amplicon or shotgun sequencing data are accepted. If you are interested in running the samples using other technologies (HiC/single-cell/etc.) please contact Michalis Hadjithomas at michalish@dnanexus.com.
  5. Users that have submitted complete protocols will be able to analyze results on Mosaic in order to:
    1. Compare differences in their protocol versus all other protocols.
    2. Visualize the results of their samples against those from all other samples.
    3. Analyze their results against the others in terms of various qualitative and quantitative metrics (For the NIST samples only.)

For groups interested in analyzing the data:

  1. Once we have a significant amount of entries, we will start implementing data freezes and enable groups to download sequencing data and metadata.
  2. Groups can analyze these data using their own tools or by creating Mosaic Apps.
  3. More details to come. Join the Challenge now to receive data freeze alerts.

For groups interested in submitting Apps to the Standards Challenge:

More information for this section will be provided when the App submission feature is released.