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SGA is implemented as a set of subcommands. The main subcommands are:

• preprocess - Prepare a set of sequence reads for assembly
• ``index``` - Build the FM index for a set of sequence reads
• merge - Merge two indices together. This can be used to build a distributed indexing pipeline.
• overlap - Find overlaps between reads to construct a string graph
• correct - Correct base calling errors in a set of reads
• rmdup - Remove duplicate sequences
• assemble - Construct contigs from a string graph

Detail usage information for each command is printed from the --help option. For example, this command will print the options for the index subprogram:

  sga index --help

Put together, the commands form an assembly pipeline. See the example workflow.