| Description |
SOAPdenovo, a short read de novo assembly tool, is a package for assembling short oligonucleotide into contigs and scaffolds. Official Homepage
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| Documentation |
Users Manual
FAQ
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
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| 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
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| How to Access the Program |
Availability
| Servers |
Versions |
Paths |
Parallelization Methods |
| Aurora |
1.04 |
/apps/SOAPdenovo/104 |
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| 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
Options
-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
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| Additional Notes |
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