SOAPdenovo¶

Description¶

SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. SOAPdenovo2 has the advantage of a new algorithm design that reduces memory consumption in graph construction, resolves more repeat regions in contig assembly, increases coverage and length in scaffold construction, improves gap closing, and optimizes for large genome. Two binaries are available: * SOAPdenovo-63mer - supports kmer length up to 63 * SOAPdenovo-127mer - supports kmer length of 63-127 * A SOAPdenovo symlink points to SOAPdenovo-63mer.

Environment Modules¶

Run module spider soapdenovo to find out what environment modules are available for this application.

Environment Variables¶

HPC_SOAPDENOVO_DIR - installation directory
HPC_SOAPDENOVO_BIN - executable directory

Categories¶

biology, ngs