Main logo
tutorial arrow
Create your own tool library
Bookmark tools and put favorites into folders to find them easily.


Provides a short-read assembly method that can build a de novo draft assembly for the human-sized genomes. SOAPdenovo 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. SOAPdenovo is made up of six modules that handle read error correction, de Bruijn graph (DBG) construction, contig assembly, paired-end (PE) reads mapping, scaffold construction, and gap closure. The major last improvements of SOAPdenovo are: i) enhancing the error correction algorithm, ii) providing a reduction in memory consumption in DBG constructions, iii) resolving longer repeat regions in contig assembly, iv) increasing assembly length and coverage in scaffolding and v) improving gap closure.

User report

tutorial arrow
Vote up tools and offer feedback
Give value to tools and make your expertise visible
Give your feedback on this tool
Sign up for free to join and share with the community

0 user reviews

0 user reviews

No review has been posted.

SOAPdenovo forum

tutorial arrow
Communicate with other users
Participate in the forum to get support for using tools. Ask questions about technical specifications.
Take part in the discussion
Sign up for free to ask question and share your advices

No open topic.

SOAPdenovo classification

SOAPdenovo specifications

Software type:
Restrictions to use:
Programming languages:
C, C++
Computer skills:
Command line interface
Operating system:
Unix/Linux, Mac OS
GNU General Public License version 2.0

SOAPdenovo distribution


tutorial arrow
Upload and version your source code
Get a DOI for each update to improve tool traceability. Archive your releases so the community can easily visualize progress on your work.
Facilitate your tool traceability
Sign up for free to upload your code and get a DOI

No versioning.


SOAPdenovo support



  • Jun Wang <>


tutorial arrow
Promote your skills
Define all the tasks you managed and assign your profile the appropriate badges. Become an active member.
Promote your work
Sign up for free to badge your contributorship



BGI HK Research Institute, Tai Po Industrial Estate, Hong Kong; HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory & Department of Computer Science, University of Hong Kong, Pokfulam, Hong Kong; School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China; School of Computer Science, National University of Defense Technology, Kaifu District, Changsha, Hunan, China

Funding source(s)

The project was supported by the State Key Development Program for Basic Research of China-973 Program (2011CB809203), National High Technology Research and Development Program of China-863 program (2012AA02A201), the National Natural Science Foundation of China (90612019), the Shenzhen Key Laboratory of Trans-omics Biotechnologies (CXB201108250096A), the Shenzhen Municipal Government of China (JC201005260191A and CXB201108250096A), and partially supported by RGC General Research Fund 10612042.

Link to literature

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.