Assemble
UCEasy has four options for assembly, SPades, Trinity, Velvet and ABySS. You can choose either of them by using the --assembler flag but the default is SPades because it works better in most cases. For the assemble command, provide a directory with the trimmed fastq files obtained in the Quality-Control step, clean-fastq in this example.
$ uceasy assemble clean-fastq/
Running this command will create the directories assemblies and assemblies/contigs with the actual contigs.
Note that the assembler to use wasn't specified, that's because SPades is the default, but you can specify it explicitly with the --assembler flag, or -a for short. The options are spades or trinity. Also, to not overwrite the assemblies directory you can give it an arbitrary name with the --output flag.
$ uceasy assemble --ouput assemblies-trinity --assembler trinity clean-fastq/
NOTE: By default, the commands use all CPU threads available but you can specify it with the --threads flag.