SOAPdenovo

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Application data

Biological application domain(s) De-novo assembly
Principal bioinformatics method(s) Assembly
Technology Illumina
Maintained? Yes
Input format(s) FASTA, FASTQ
Software features Has a modular structure and comes with a read corrector, an assembly module, a scaffolder and a gap filler
Licence GPLv3
Operating system(s) Linux, Mac OS X

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

SOAPdenovo is a set of software tools that can be used for assembling (large) genomes. It is built to run on one machine but is built multi-threaded and will thus be able to finish the assembly process in a reasonable time frame. The current publicly available version is 1.05 however version 1.06 has been used by BGI for assembling the genome of the bacteria causing EHEC see the supplement in http://www.nejm.org/doi/full/10.1056/NEJMoa1107643#t=article for details. Link: http://soap.genomics.org.cn/soapdenovo.html Category: Assembly (de novo)

Links


References

  1. Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Yang H, Wang J. 2009. Genome Research


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