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SOAPdenovo specifications

Information


Unique identifier OMICS_00031
Name SOAPdenovo
Alternative name SOAPdenovo2
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, C++
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.0
Stability Stable
Requirements
GCC
Maintained Yes

Subtool


  • GapCloser

Download


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Versioning


No version available

Documentation


Maintainers


  • person_outline Jun Wang
  • person_outline SOAPdenovo Team

Additional information


https://sourceforge.net/projects/soapdenovo2/

Publications for SOAPdenovo

SOAPdenovo citations

 (757)
library_books

Comparison of the Chinese bamboo partridge and red Junglefowl genome sequences highlights the importance of demography in genome evolution

2018
BMC Genomics
PMCID: 5941490
PMID: 29739321
DOI: 10.1186/s12864-018-4711-0

[…] of 70. We corrected possible sequencing errors based on the distribution of Kmer frequencies using SOAPec v2.01 with default settings []. We then built de novo assemblies from the edited reads using SOAPdenovo2 v2.04 [] and ABySS v1.9.0 []. We also assembled the genome with MaSuRCA v2.3.2 [], which uses its own raw data quality control tools. For computational feasibility, the three assemblies us […]

library_books

Extensive gene rearrangements in the mitochondrial genomes of two egg parasitoids, Trichogramma japonicum and Trichogramma ostriniae (Hymenoptera: Chalcidoidea: Trichogrammatidae)

2018
Sci Rep
PMCID: 5935716
PMID: 29728615
DOI: 10.1038/s41598-018-25338-3

[…] eqPrep (https://github.com/jstjohn/SeqPrep). Sickle (https://github.com/najoshi/sickle) was applied to conduct reads trimming with default parameters to obtain clean data for this study. In addition, SOAPdenovo (http://soap.genomics.org.cn/, v2.05) was used to perform genome assembly with multiple Kmer parameters and assess the assembly results. GapCloser software (downloaded from SOAPdenovo websi […]

library_books

Comparative genomic analysis of multidrug resistant Streptococcus pneumoniae isolates

2018
PMCID: 5939923
PMID: 29765237
DOI: 10.2147/IDR.S147858

[…] vo assembled with Newbler 2.9 (version 20130529_1641) (http://www.454.com/products/analysis-software/). Gaps inside the scaffold were closed with GapCloser (version 1.12) (http://soap.genomics.org.cn/soapdenovo.html). All newly sequenced genomes were ordered on the basis of the reference genome with Mauve (version 2.3.1). For each genome, regions that were absent in the reference genome were extra […]

library_books

Genome Sequencing and Analysis of the Peanut B Genome Progenitor (Arachis ipaensis)

2018
Front Plant Sci
PMCID: 5943715
PMID: 29774047
DOI: 10.3389/fpls.2018.00604

[…] formed under the HiSeq2500 Sequencing System with 11 paired-end sequencing libraries, including 250, 500, 800 bp, 2, 5, 10, and 20 Kb using the standard protocol provided by Illumina (San Diego, USA).SOAPdenovo2 (version 2.04.4) (Luo et al., ) was employed with optimized parameters to construct contigs and original scaffolds as previous described (Chen et al., ). Subsequently, SSPACE (version 2.0) […]

library_books

Novel sequences, structural variations and gene presence variations of Asian cultivated rice

2018
Sci Data
PMCID: 5931083
PMID: 29718005
DOI: 10.1038/sdata.2018.79

[…] Novel sequences absent in the reference genome were derived from the de novo assemblies of the 3,010 rice accessions. To achieve high-quality assemblies, we utilized a method with iterative use of SOAPdenovo r240 to select the best Kmer parameter for each accession. In detail, we first determined an initial Kmer (Kinit) for rice accession R based on a linear model Kinit=ROUND(a*DepR+b), where D […]

call_split

Whole genome de novo sequencing reveals unique genes that contributed to the adaptive evolution of the Mikado pheasant

2018
GigaScience
PMCID: 5941149
PMID: 29722814
DOI: 10.1093/gigascience/giy044
call_split See protocol

[…] [] both with default parameters, JR (version 1.0.4; parameters: “-minOverlap 60 -maxOverlap 90 -ratio 0.3”) [], SGA (version 0.10.13; parameters: “assemble -m 125 -d 0.4 -g 0.1 -r 10 -l 200”) [], and SOAPdenovo (version 2.04; parameters: “-K 47 -R”) [] were also used to assemble contigs. We employed SSPACE (SSPACE, RRID:SCR_005056, version 3.0; parameter: “-z 300”) [] to construct scaffolds for th […]

Citations

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SOAPdenovo institution(s)
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
SOAPdenovo 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.

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