The major subcommands of SGA 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
• fm-merge - Efficiently merge reads that can be unambiguously assembled
• correct - Correct base calling errors in a set of reads
• filter - Remove duplicate and low quality 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