SOAPdenovo protocols

View SOAPdenovo computational protocol

SOAPdenovo statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Genome assembly Gap closing Assembly scaffolding chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

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


Versioning


Add your version

Documentation


Maintainers


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

Additional information


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

Publications for SOAPdenovo

SOAPdenovo in pipelines

 (247)
2018
PMCID: 5767256
PMID: 29375524
DOI: 10.3389/fmicb.2017.02659

[…] sequenced using illumina hiseq 3000 (illumina, san diego, ca, united states). a total of 29,226,076 trimmed reads were obtained. the sequence assembly and optimization procedures were conducted by soapdenovo2 software (). possible open reading frames (orfs) were predicted by genemark software (). functional annotation of orfs and homology assignments between genes from phage sh-ab 15519 […]

2018
PMCID: 5805866
PMID: 29439028
DOI: 10.1128/genomeA.00002-18

[…] sequenced by using the illumina hiseq 2000 platform (majorbio co., ltd., shanghai, china). paired-end reads with an average length of 500 bp and total read size of ~300 mbp were assembled by using soapdenovo version 2.04 (), and gap filling between contigs and the remaining gaps between scaffolds were closed by using gapcloser version 1.12 ()., the assembled draft genome contained 4,710,590 bp […]

2018
PMCID: 5824003
PMID: 29472338
DOI: 10.1128/genomeA.00087-18

[…] reads (180-bp and 800-bp libraries) were generated to reach a 398-fold depth of coverage using the illumina hiseq 2000 platform (illumina, inc., san diego, ca, usa). the reads were assembled using soapdenovo version 1.05 (, ). the resulting genome sequence of alcanivorax sp. 97co-6 comprises 43 contigs (n90 = 78,739), with 3,253,423 bp and an average g+c content of 54.53%. gene annotation […]

2018
PMCID: 5843717
PMID: 29519820
DOI: 10.1128/genomeA.00067-18

[…] confirmed as virulent on the basis of animal experiments (). the complete genome sequence was determined by the illumina hiseq platform at novogene (beijing, china). assembly was performed using soapdenovo. gaps were filled by primer walking and sequencing of pcr products. the assembly of the genome was further verified by pcr. coding sequences (cds) were predicted using glimmer 3.02 […]

2018
PMCID: 5904165
PMID: 29666397
DOI: 10.1038/s41598-018-24443-7

[…] the genomic dna of c. neopsychrotolerans sl-16 was extracted using the ctab method. the 500-bp insert library was sequenced using the illumina pe250 system. the clean reads were then assembled by soapdenovo (http://soap.genomics.org.cn, v2.04) for data processing. genes were subsequently predicted using augustus 3.2.1 and genemark-es 4.21 with default parameters, which were further integrated […]


To access a full list of citations, you will need to upgrade to our premium service.

SOAPdenovo in publications

 (1324)
PMCID: 5946483
PMID: 29747580
DOI: 10.1186/s12864-018-4739-1

[…] respectively. low-quality reads were filtered by trimmomatic []. the high-quality reads were used for de novo assembly and scaffolding using soap denovo (version 1.05, http://soap.genomics.org.cn/soapdenovo.html). gaps closure was performed using gapcloser v1.12 [, ]. the completeness of the c. pseudoreteaudii genome was evaluated using cegma []. repeat sequences were identified […]

PMCID: 5943271
PMID: 29743477
DOI: 10.1038/s41467-018-04298-2

[…] with appropriate antibiotics., the whole-genome sequencing of nodulisporium sp. (no. 65-12-7-1) was performed by sangon biotech co., ltd. (shanghai, china) with an illumina hiseq 2500 system. the soapdenovo version 2.04 (http://soap.genomics.org.cn/soapdenovo.html) sequence assembly system was used to produce 381 contigs, covering ~36.9 mb. gene prediction was then performed with augustus […]

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 […]

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

[…] 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 […]

PMCID: 5943715
PMID: 29774047
DOI: 10.3389/fpls.2018.00604

[…] representing 149.53 × genome coverage, with fragment lengths ranging from 250 to 20 kb (supplementary file : table s1). a total of ~1,391.70 mb of the a. ipaensis genome sequence was assembled using soapdenovo2 (luo et al., ) with a contig n50 of 8,067 bp and a scaffold n50 of 170,050 bp (table ; supplementary file : tables s2, s3). an assessment of the draft genome assembly using the core […]


To access a full list of publications, you will need to upgrade to our premium service.

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.

SOAPdenovo reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review SOAPdenovo