How to use Phaster for bacteriophage data analysis

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Phaster is a bioinformatics tool for analyzing bacteriophage sequencing data sets.  It generates a variety of annotation and phage identification results that are very useful for interpreting phage sequencing data.

 

Instructions for using Phaster with sequencing data

The Sequencing Center will provide you with FastA formatted de novo assembly files.  These files will be available in your Box.com account in an “Assembly” directory. The assembly filenames will include the text “…..scaffolds.fasta”. You will use the assembly files in Phaster.

  1. Go to your Box.com “Assembly” directory.  Download the assembly file(s) that you want to analyze to your local workstation.  
  2. Go to Phaster.
  3. Under “Select an input type” click “Upload File”.  
  4. Click “Choose File”.  Navigate to the location where you stored the assembly file(s) on your workstation.  “Choose” one FastA file for analysis.
  5. Click the checkbox “My FASTA file consists of metagenomic contigs”.
  6. Click “Submit”.

For most bacteriophage data sets, Phaster will run for a few minutes.  The tool will display run progress in a separate webpage. When Phaster is done it will display a “Submission Results” page.  The results are fairly extensive and cannot be covered in detail in this short note. Please see the Phaster Help webpage and Phaster Ouput webpage for more information about how to interpret the results.