From SEQwiki
Jump to: navigation, search

Application data

Biological application domain(s) De-novo assembly
Principal bioinformatics method(s) Sequence 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 for details. Link: Category: Assembly (de novo)



  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

To add a reference for SOAPdenovo, enter the PubMed ID in the field below and click 'Add'.

[ edit box ]

Search for "SOAPdenovo" in the SEQanswers forum / BioStar or:

Web Search Wiki Sites Scientific
Personal tools

wiki navigation
vBSSO Login Form

Reset Password
Single Sign On provided by vBSSO