Reference-guided workflows vary in the number and contents of output files and folders. Only a subset of items in the table below may appear for a particular workflow.

In the file names below, the project name should be understood to precede any hyphen (-) or period (.) used at the beginning of file and folder names.

Single assemblies:

The project folder has the name specified in the Assembly Output screen and contains:

  • .script file
  • .assembly package (called .transcriptome for the transcript annotation workflow)
  • -noSplit.assembly package (Reference-guided assembly with gap closure workflows only)
  • -Reports folder
    • -zinternal folder
      • info folder


All Exome and Gene Panel projects and multiple sample assemblies run as separate assemblies:

The project folder contains the name specified in the Assembly Output screen followed by the suffix _assemblies (called _RNA-Seq in the RNA-Seq reference-guided workflow). This folder contains:

  • .script file (if saved in the “Your assembly is ready to begin” screen).
  • Results.txt file - Overview information and statistics for each assembly.
  • .table.txt file
  • .template.script file
  • _arstar.script file – A script to load all assemblies as a SNP project in ArrayStar.
  • _arstarValidation.script file – (only if validation control was present) A script to load the validation control assembly and associated VCF file as a SNP project in ArrayStar and to automatically calculate the accuracy statistics.
  • .assembly packages (one per sample)
  • -Reports folders (one per sample)
    • -zinternal folder
      • info folder

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