All modules for which code is available

• assemble.Assemble_Command
• assemble.Assemble_Program_Pear
• classes.ChewbaccaCommand
• classes.ChewbaccaProgram
• classes.ProgramRunner
• clean.Clean_Adapters_Command
• clean.Clean_Adapters_Program_Flexbar
• clean.Clean_Deep_Command
• clean.Clean_Deep_Program_Macse
• clean.Clean_Deep_Repair_Command
• clean.Clean_Deep_Repair_Program_Macse
• clean.Clean_Quality_Command
• clean.Clean_Quality_Program_Trimmomatic
• cluster.Cluster_Command
• dereplicate.Dereplicate_Command
• dereplicate.Dereplicate_Program_Vsearch
• otu.Annotate_OTU_Table_Command
• otu.Build_OTU_Table_Command
• otu.Query_OTU_DB_Command
• otu.Query_OTU_Fasta_Command
• preclean.Preclean_Command
• preclean.Preclean_Program_Bayeshammer
• rename.Rename_Command
• util.Convert_Fastq_Fasta_Command
• util.Merge_Command
• util.Partition_Command
• util.Ungap_Command