SOAPdenovo pipeline

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

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Documentation


Maintainers


  • person_outline Jun Wang <>
  • person_outline SOAPdenovo Team <>

Additional information


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

Publications for SOAPdenovo

SOAPdenovo citations

 (31)
2017
PMCID: 5597748

[…] using illumina hiseq 2000 sequencing technology. a 468-bp illumina paired-end library produced 5,934,226 reads (read length, 90 bp) totaling 502 mb. the short reads were assembled into genomes using soapdenovo, version 2.04 (3), resulting in 17 contigs. the protein-coding open reading frames (orfs) were predicted using glimmer version 3.02 (4), trna genes were predicted using trnascan-se 1.2 […]

2017
PMCID: 5309792

[…] software, bgi)., the obtained clean data were used to perform the metagenome sequences. before assembly, k-mer analysis (k-mer length 15) was done to evaluate the sequencing depth for each sample. soapdenovo (version 1.06)73 was used to assemble filtered data in contigs and scaffolds and assembly results were optimized by in-house scripts (key parameters: -r 2; -l 35; -m 4; -p 1) using […]

2017
PMCID: 5270707

[…] the libraries used were three illumina paired-end (500 bp, 2,000 bp, and 6,000 bp inserted size) and one pacbio mate pair 5k/6k. to estimate the genome size, k-mer analysis was performed. afterward, soapdenovo v2.04 software was employed to assemble the reads after filtering, while soapsnp, soapindel, and gatk were applied for error correction. furthermore, whole-genome optical mapping generated […]

2017
PMCID: 5256215

[…] of both paired-end and mate-pair reads was performed using an in-house program. after this step, illumina pcr adapter reads and low-quality reads were filtered. the filtered reads were assembled by soapdenovo (2, 3) to generate 46 contings, and the assembly falls to 14 scaffolds., transfer rna (trna) genes, ribosomal rna (rrna) genes, and small rnas (srnas) were predicted with trnascan-se (4), […]

2016
PMCID: 5084872

[…] construction and sequencing reactions were performed according to the manufacturer’s instructions and a 300 pair-end library was generated. the resulting sequences were de novo assembled using soapdenovo v2.01 (http://soap.genomics.org.cn/) (6). for the prokaryotic organism, we used an ab initio prediction method to get gene models for strain av208. gene models were identified using […]

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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