Reference-guided workflow output

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 reference-guided RNA-seq workflows). This folder contains:

• .script file (if saved in the Run Assembly 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