Option	Description
[-p]	Flag to specify SFF data in filedesc comes from Paired End sequencing. If the “-p” option is not given, auto-detect will be used to determine the type of each Read Data set. Auto-detect will determine the presence or absence of the Paired End linker sequence: if at least 25% of the first 500 reads in the file (or 25% of all the reads if there are fewer than 500 reads in the file) contain the linker, the file is recognized as a Paired End file.
[-lib libname]	This option specifies that the default Paired End library for each of these files should be the string “libname”. It can be used to group together the Paired End reads from different files, so that they are all used together in calculating a mean distance between the halves of each Paired End pair of reads. (By default, each SFF file is treated as a separate library, and a separate mean Paired End distance is calculated for each.)
[-mcf filename]	This option specifies an MID configuration file (other than the default file) to be used by the assembly for decoding the multiplex information appearing on the command line.

External files: • GS Read Data files (SFF files) are not copied to the project directory. A symbolic link to the file is created and placed in the project’s sff directory. Thus, if the original file is moved or erased from the file system, the project will not operate correctly. This applies whether the files are added via the GUI or the command line. • FASTA/FASTQ files are not copied to the project directory. The file path is recorded in the project setup. Thus, if the original file is moved or erased from the file system, the project will not operate correctly. This applies to all instances of FASTA/FASTQ files that can be added to an Assembly or Mapping project, whether done via the GUI or the command line: ◦ FASTA/FASTQ reads files, including Sanger reads ◦ Trimming database files ◦ Screening database files   Unlike with the GS Read Data files, no symbolic link to the file is created for FASTA/FASTQ files

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