Community Analysis Workflow

PMI Workflow - Community Analysis


These workflows are intended to preserve and share records and data from DNA sequence based microbial community analyses for the PMI project.  Primarily these will include rRNA gene ampli5=1con sequencing generated by pyrosequence based analysis, but may also include important protein coding genes (e.g. AmoA - ammonia monooxygenase) or Sanger sequence based information. In the form of a workflow we have outlined five basic steps typically used in completing a community analysis and provide fields to fill in to preserve records as well as ability to upload data files associated with the analysis.

Step 1:

This step includes generic information on the experiment such as PI, experimenter, technician etc.  Please add a short note on the purpose of the experiment as well as any extra information into the notes/comments section as required.  Experimental design details can also be added as uploaded files.    

Title:
General Experiment Details
  1. Entered Date
  2. Experiment Name
  3. Experimentor / Analyst
  4. Associated PIs
  5. Comments
Step 2:
This step should include details regarding the extraction of DNA from samples.  An excel or tab delimited file should also be included listing yield and quality information.    

Title: DNA Extraction.
  1. Method / Kit
  2. Date
  3. Technician / Experimentor
  4. Notebook Reference
  5. Extraction results file (File Upload - TAB del - Mandatory - Parsable)
  6. Comments
Step 3:
Please include in this step information about the primary amplicon generation and PCR conditions, primers sequences used, etc.  An excel or tab delimited file that includes the primer barcoding information for each sample should be uploaded below.  Also upload any information about PCR yields and quality for each amplicon if available.    

Title: PCR Amplification
  1. Date
  2. Technician / Experimentor
  3. Notebook Reference
  4. Conditions
  5. Primer Set / Region
  6. Amplicon Quantification
  7. Primer barcode-sample File Upload ( File Upload - TAB del - Optional - Nonparsable)    
  8. Quantification Files Upload ( File Upload - TAB del - Optional - Nonparsable)
  9. Comments
Step 4:
Please include in this section information relevant to the sequencing of the PCR amplicons including instrument type, protocol/kit version information.  Also upload raw output files from the sequencer (e.g FastQ or SFF files).   

Title: Sequencing
  1. Instrument Type ( Controlled Vocabulary - 454, Sanger, Miseq, Hiseq, -- other (add entry when selected) )
  2. Reagent Type / Chemistry
  3. Vendor Software Version
  4. Internal Standard(s)
  5. Primer Set
  6. Sequencing Output Files ( File Upload - SSF/FastQ - Mandatory - Nonparsable - Project Open)
  7. Comments
Step 5:
This step should include information on quality control, denoising, etc. as well as files generated from this initial processing (e.g. trimmed and chimera checked dataset).  Also files for OTU assignments for the data sets generated should be uploaded (OTUxEnv Table, BIOME file, OTU representative fasta file).   

Title: Analysis
  1. Program Type ( Controlled Vocabulary - Qiime, Mothur, )
  2. Program Version
  3. Date
  4. Experimentor
  5. Denoising / QAQC Methods
  6. Quality Controlled Dataset (File Upload - TAB del - Mandatory - NonParsable - Project Open)    
  7. OTU By Environment Table (File Upload - TAB del - Mandatory - NonParsable - Project Open)
  8. OTU Representative Sequence file ( File Upload - FASTA - Mandatory - NonParsable - Project Open)
  9. BIOME File ( File Upload - TAB del - Optional - NonParsable - Project Open)
  10. Taxonomy File ( File Upload - PDF - Optional - NonParsable - Project Open)
  11. Comments

Last Modified Date: June 2nd 2013