Data Analysis Applications Results

1.3.3

As indicated above, the data analysis applications are often performed on a pool of sequencing Runs rather than on any single Run, and/or can require additional information beyond the Run data. For this reason, they are carried out off-instrument, via a Graphical User Interface (GUI) or from the command line on a DataRig, rather than on the GS FLX+ Instrument. For the GS Junior System, this can also be performed on a separate computer resource (DataRig) but it is typically performed on the Attendant PC, though still separately from the data acquisition / data processing.

As a consequence of this separation, the result files generated by these applications are not deposited in a Run folder. For the GS De Novo Assembler and the GS Reference Mapper, rather, one of the following will apply:

•

A folder with a ‘P_’ prefix (for ‘P’ost-Run Analysis) is created to receive them, in the user’s current working directory on the DataRig or GS Junior Attendant PC at the time the application is launched, or written to a directory specified by the user via the applications’ GUI or on the command line.

•

Mapping and Assembly can also be carried out in a “project-based” fashion, whereby data sets can be added to existing results (or a new reference sequence can be specified) for an existing Assembly or Mapping “project”. This uses the corresponding applications’ GUI (or can be done using the newAssembly, newMapping, and associated commands), and the data is then stored in a “Project” folder. A Project folder is identified by the “454Project.xml” file it contains.

The folder and file structures generated for each of these commands (or GUI equivalents) are shown in the Figures below: the “one-step” runAssembly (Figure 4) or runMapping (Figure 5) commands, for the “standard”, non-incremental assembly or mapping of one or more Runs; and newAssembly (Figure 6) or newMapping (Figure 7), for the “project-based”, incremental assembly or mapping of one or more Runs. See Part C, Sections 1 and 2 of this manual for full file descriptions and for more information on the GS De Novo Assembler and GS Reference Mapper applications.

The GS Amplicon Variant Analyzer application can also operate either via a GUI or via its own Command Line Interface (the AVA-CLI), but its output is not structured like that of the other two data analysis applications. See Part D of this manual for details on this application.

$[current_working_directory] or [directory_specified]
   P_yyyy_mm_dd_hh_min_sec_runAssembly/
      454AllContigs.fna
      454AllContigs.qual
      454LargeContigs.fna
      454LargeContigs.qual
      454NewblerMetrics.txt
      454NewblerProgress.txt
      454AlignmentInfo.tsv
      454ContigGraph.txt
      454PairAlign.txt
      454ReadStatus.txt
      454Contigs.ace or ace/ContigName.ace or consed/…
      sff/
         *.sff
      454Scaffolds.fna¹
      454Scaffolds.qual¹
      454Scaffolds.txt¹

Figure 4: File output of the GS De Novo Assembler application, using the runAssembly command (or its GUI equivalent). All result files (specifying the actual contig names) are placed in a folder with a ‘P_’ prefix, within the user’s current working directory when running the command or in a directory specified by the user. All input SFF files used in the assembly are organized in the sff sub-directory. ¹These files are produced only when the Paired End option is used; the Paired End option also adds sections to the 454NewblerMetrics.txt file. See Part C, Section 1 of this manual for full file descriptions.

$[current_working_directory] or [directory_specified]
   P_yyyy_mm_dd_hh_min_sec_ runMapping /
      454AllContigs.fna
      454AllContigs.qual
      454LargeContigs.fna
      454LargeContigs.qual
      454AllDiffs.txt
      454HCDiffs.txt
      454NewblerMetrics.txt
      454NewblerProgress.txt
      454MappingQC.xls
      454AlignmentInfo.tsv
      454PairAlign.txt
      454ReadStatus.txt
      454RefStatus.txt
      454Contigs.ace or ace/refaccno.ace or consed/…
      sff/
         *.sff

Figure 5: File output of the GS Reference Mapper application, when using the runMapping command (or its GUI equivalent). All result files (specifying the actual reference sequence accession numbers) are placed in a folder with a ‘P_’ prefix, within the user’s current working directory when running the command or in a directory specified by the user. All input SFF files used in the mapping are organized in the sff sub-directory. See Part C, Section 2 of this manual for full file descriptions.

$[current_working_directory] or [directory_specified]
   P_yyyy_mm_dd_hh_min_sec_runAssembly/
      assembly/
         454AllContigs.fna
         454AllContigs.qual
         454LargeContigs.fna
         454LargeContigs.qual
         454NewblerMetrics.txt
         454NewblerProgress.txt
         454AlignmentInfo.tsv
         454ContigGraph.txt
         454PairAlign.txt
         454ReadStatus.txt
         454Contigs.ace or ace/ContigName.ace or consed/…
         454AssemblyProject.xml
         454Scaffolds.fna¹
         454Scaffolds.qual¹
         454Scaffolds.txt¹
      sff/
         *.sff
      454Project.xml

Figure 6: File output of the GS De Novo Assembler application, when using the newAssembly and related commands (or their GUI equivalents) for “project-based” assembly. All result files (specifying the actual contig names) are placed in a folder within the user’s current working directory when running the command or in a directory specified by the user. This is identified as a “Project” folder by the presence of a 454Project.xml file within it. All assembly status and result files are organized in the assembly sub-folder; and all input SFF files used in the assembly (or symbolic links to them) are organized in the sff sub-folder. ¹These files are produced only when the Paired End option is used; the Paired End option also adds sections to the 454NewblerMetrics.txt file. See Part C, Section 1 of this manual for full file descriptions.

$[current_working_directory] or [directory_specified]
   P_yyyy_mm_dd_hh_min_sec_ runMapping/
      mapping/
         454AllContigs.fna
         454AllContigs.qual
         454LargeContigs.fna
         454LargeContigs.qual
         454AllDiffs.txt
         454HCDiffs.txt
         454NewblerMetrics.txt
         454NewblerProgress.txt
         454MappingQC.xls
         454AlignmentInfo.tsv
         454PairAlign.txt
         454ReadStatus.txt
         454RefStatus.txt
         454Contigs.ace or ace/ContigName.ace or consed/…
         454MappingProject.xml
      sff/
         *.sff
      454Project.xml

Figure 7: File output of the GS Reference Mapper application, when using the newMapping and related commands (or their GUI equivalents) for “project-based” mapping. All result files (specifying the actual reference sequence accession numbers) are placed in a folder within the user’s current working directory when running the command or in a directory specified by the user. This is identified as a “Project” folder by the presence of a 454Project.xml file within it. All mapping status and result files are organized in the mapping sub-folder; and all input SFF files used in the mapping (or symbolic links to them) are organized in the sff sub-folder. See Part C, Section 2 of this manual for full file descriptions.