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SOAPdenovo, a short read de novo assembly tool, is a package for assembling short oligonucleotide into contigs and scaffolds.

Official Homepage
Users Manual

System Requirement
SOAPdenovo aims for large plant and animal genomes, although it also works well on bacteria and fungi genomes. It runs on 64-bit/32-bit Linux/MAC OS systems with a minimum of 5G physical memory. For big genomes like human, about 150 GB memory would be required 
License Agreement and Citation Format
License Agreement
GPL ver. 3

Citation Format 
Li et al. (2008) SOAP: short oligonucleotide alignment program" . BIOINFORMATICS, 24 no.5,713–714, doi:10.1093/bioinformatics/btn025

How to Access the Program 
Servers Versions Paths Parallelization Methods
Aurora 1.04 /apps/SOAPdenovo/104  
Using the Program
Once the configuration file is available, the simplest way to run the assembler is:
./soapdenovo all -s config_file -o output_prefix

User can also choose to run the assembly process step by step as:
./soapdenovo pregraph -s config_file -o output_prefix
./soapdenovo contig -g output_prefix
./soapdenovo map -s config_file -g output_prefix
./soapdenovo scaff -g output_prefix

-s STR configuration file
-o STR output graph file prefix
-g STR input graph file prefix
-K INT K-mer size [default 23]
-p INT multithreads, n threads [default 8]
-R use reads to solve tiny repeats [default no]
-d remove low-frequency K-mers with single occurrence [default no]
-D remove edges comprised by entirely single frequency K-mers [default no]
-F intra-scaffold gap closure [default no]
-L minimum contigs length used for scaffolding
-a initMemoryAssumption: Initiate the memory assumption to avoid further reallocation

Output files
These files are output as assembly results:
*.contig contig sequence file
*.scafSeq scaffold sequence file

Additional Notes
Last Updated - 29th Sep 2011
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