Specifying information about the outputs

-o <file> / --output <file> Give the name for the file that will contain the contigs, in fasta format, that are assembled.

This parameter is required.

-m <n> / --min-length <n> Set the minimum length for contigs to be output from the assembly process. The default value is 200 bases.

-f <file> / --feature_output <file>

Providing this option indicates that the annotations associated with scaffolding should be output.

The output can be in GFF format (the default), or in AGP format. The file suffix you provide specifies the output format. For AGP format, use '.agp'. For gff format, you can use whatever name you like, but it would be usual to use the filename suffix '.gff'.