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SGA is a de novo assembler designed to assemble large genomes from high coverage short read data. It is designed as a modular set of programs, which are used to form an assembly pipeline. A description of the SGA design is found here.

When first learning SGA, it is highly recommended to run one of the example assemblies from the src/examples directory to become familiar with the flow of data through the program. A page containing frequently asked questions can be found here.

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
• correct - Correct base calling errors in a set of reads
• rmdup - Remove duplicate sequences
• qc - Remove possible chimeric reads
• 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