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SOAPdenovo (Short Oligonucleotide Analysis Package de novo) 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. Now the new version is available. SOAPdenovo2, which 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.


Usage

To use SOAPdenovo load the relevant module

module load SOAPdenovo2/2.41

This will add the directory containing the binaries to your PATH.