saveProject - User Guide to SeqMan NGen

The saveProject command saves the assembly to a project file. By default, the SeqMan Pro / SeqMan Ultra project file format (.sqd) is used. Phrap (.ace) and FASTA (.fas) formats may also be specified by using the format parameter, and specifying the desired file extension using the file parameter.

Parameter	Description	Allowed values
file	(required) Specifies the directory and file name of the project file to be saved.	[directory/filename enclosed in quotes]
format	Specifies the output file format. SeqMan - Saves a 64-bit SeqMan Pro project file (.sqd) that is compatible with SeqMan Ultra or SeqMan Pro version 8.1 and higher (default). SeqMan8 - Saves a 32-bit SeqMan Pro project file (.sqd) that is compatible with SeqMan Ultra or SeqMan Pro version 8.0 and higher. SeqMan7 - Saves a 32-bit SeqMan Pro project file (.sqd) that is compatible with SeqMan Ultra or SeqMan Pro version 7.2 and higher. Note that this project file will be much bigger than the same project created in either of the SeqMan formats listed above. Phrap - Saves an .ace file. Fasta - Saves .fas and .qual files of the consensus sequence for each contig. BAM - Saves a BAM file (SNG/SMNG reference-guided assemblies only). SAM - Saves a SAM file (SNG/SMNG reference-guided assemblies only).	[SeqMan\|SeqMan8\|SeqMan7\|Phrap\|Fasta\|BAM\|SAM]
onePackage	Specifies whether an assembly containing multiple reference sequences should be bundled into a single .assembly package. If ‘false’ is entered, one .assembly package is created per contig.	[true\|false]
openInSeqMan	Specifies whether to automatically launch SeqMan Pro / SeqMan Ultra and open the completed assembly once the script has completed.	[true\|false]

Example:

SaveProject
   file: “/Library/My projects/ABC_project.sqd”
   format:seqman
   openInSeqMan:true

runScript

saveReport

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