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SOAPsv specifications


Unique identifier OMICS_04230
Name SOAPsv
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Version 1.02
Stability Stable
gcc compiler
Maintained Yes


  • Primates
    • Homo sapiens


No version available


  • person_outline SOAP3
  • person_outline Jian Wang

Publication for SOAPsv

SOAPsv citations


Deep whole genome sequencing of 90 Han Chinese genomes

PMCID: 5603764
PMID: 28938720
DOI: 10.1093/gigascience/gix067

[…] an Chinese genomesProject home page: system(s): LinuxProgramming language: Shell, Perl, Java, and C++Other requirements: BWA, 0.6.1; SOAPsv, 1.02; SOAPdenovo2; PINDEL, 0.2.4t; cnvnator, 0.2.7; Breakdancer-max, 1.2; Genome STRIP, v. 1.0; SAMtools, 0.1.18; Picard, 1.61; GATK, 2.7; BEAGLE, v. 3License: GNU General Public License v.3.0 […]


Genome wide sequencing of longan (Dimocarpus longan Lour.) provides insights into molecular basis of its polyphenol rich characteristics

PMCID: 5467034
PMID: 28368449
DOI: 10.1093/gigascience/gix023

[…] g sequence data were uniquely aligned to the reference longan genome. SNPs, indels, and sequence variations were identified using SOAPsnp (, SOAPindel [], and SOAPsv [].We used all and high-quality SNPs to infer the phylogeography and population structure for D. longan. A phylogenetic tree was subsequently generated using the neighbor-joining method impleme […]


An ethnically relevant consensus South Korean reference genome is a step towards personal reference genomes

Nat Commun
PMCID: 5123046
PMID: 27882922
DOI: 10.1038/ncomms13637

[…] e conducted whole-genome alignments between each assembly and GRCh38 using LASTZ. Then, the whole-genome alignment results were corrected and re-aligned based on a dynamic-programming algorithm using SOAPsv package. SVs that could be derived from possible misassembles were filtered out by comparing the S/P ratio for each SV region in the assembly and GRCh38; authentic SVs would be covered by suffi […]


The Genome of a Mongolian Individual Reveals the Genetic Imprints of Mongolians on Modern Human Populations

Genome Biol Evol
PMCID: 4540083
PMID: 25377941
DOI: 10.1093/gbe/evu242

[…] nce genome using the BLAT program. The mapped scaffolds were then aligned to the human reference genome again by using the LASTZ program () for precise mapping. SV candidates were called by using the SOAPsv program ( Large insertions/deletions (>100 bp), the largest proportion of the SV candidates, were finally filtered by S/P ratio (number of single-end mapped reads/n […]


Re sequencing and genetic variation identification of a rice line with ideal plant architecture

PMCID: 5520836
PMID: 27234240
DOI: 10.1186/1939-8433-5-18

[…] tive depth of 13× coverage was achieved (Table ), and the resulting consensus sequence covered approximately 82.57% of the reference genome.Genome-wide variations were then examined via SOAPsnp11 and SOAPsv using a conservative quality filter pipeline (Li et al. []), and 307 627 SNPs, 57 372 InDels, and 3 096 SVs were yielded from the 7302R genome (Table , Additional files and ). We have previous […]


Identification of Genome Wide Variations among Three Elite Restorer Lines for Hybrid Rice

PLoS One
PMCID: 3285608
PMID: 22383984
DOI: 10.1371/journal.pone.0030952

[…] ion covered approximately 84.8% of the reference genome (84%–85.99%), indicating a close relationship between the samples and cultivar 9311.SNPs, InDels, and SVs were then examined with SOAPsnp11 and SOAPsv using a conservative quality filter pipeline , yielding 267,383 SNPs from the genome of IR24, 288,764 SNPs from that of MH63, and 259,862 SNPs from that of SH527 (, […]


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SOAPsv institution(s)
BGI-Shenzhen, Shenzhen, China; School of Bioscience and Biotechnology, South China University of Technology, Guangzhou, China; Department of Computer Science, The University of Hong Kong, Hong Kong, China; Genome Research Institute, Shenzhen University Medical School, Shenzhen, China; Institute of Human Genetics, University of Aarhus, Aarhus, Denmark; Department of Biology, University of Copenhagen, Copenhagen, Denmark; Department of Genomics of Common Disease, School of Public Health, Imperial College London, London, UK; Department of Epidemiology and Biostatistics, School of Public Health, Imperial College, London, UK; The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
SOAPsv funding source(s)
Supported by a National Basic Research Program of China (973 program no. 2011CB809200), the National Natural Science Foundation of China (30725008; 30890032; 30811130531; 30221004), the Chinese 863 program (2006AA02Z177; 2006AA02Z334; 2006AA02A302;2009AA022707), the Shenzhen Municipal Government of China (grants JC200903190767A; JC200903190772A; ZYC200903240076A; CXB200903110066A; ZYC200903240077A; ZYC200903240076A and ZYC200903240080A), the Ole Rømer grant from the Danish Natural Science Research Council and the Shenzhen Municipal Government and the Local Government of Yantian District of Shenzhen.

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