SOAPsv protocols

View SOAPsv computational protocol

SOAPsv 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 Structural variant detection Deletion detection Insertion detection Inversion detection chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

SOAPsv specifications

Information


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
Requirements
gcc compiler
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Versioning


Add your version

Maintainers


  • person_outline SOAP3 <>
  • person_outline Jian Wang <>

Publication for SOAPsv

SOAPsv in pipelines

 (4)
2016
PMCID: 4870249
PMID: 27242868
DOI: 10.3389/fpls.2016.00667

[…] stop codons or splice sites. snps in coding sequences were annotated as synonymous or non-synonymous. go or pfam annotation of genes was also conducted., structural variations were detected using soapsv (version 1.02), for indel (more than 5 bp in length), replication, reversion, transposition, and other variations. the minimum read depth was set to 3., we first calculated the distances […]

2016
PMCID: 4991830
PMID: 27106267
DOI: 10.1093/dnares/dsw017

[…] the reference and unmapped reads. average sequencing depth and coverage were calculated using the alignment results. the mapped reads were then used to detect snps, indels, and svs using soapsnp and soapsv software with default parameter settings.– the snps identified were filtered based on the following stringent criteria: no less than two times for coverage depth (no less than three times […]

2016
PMCID: 5159902
PMID: 27982107
DOI: 10.1038/srep38636

[…] for identifying reads with abnormal insert sizes, or only one end mapped to the genome and determined a sv when more than 3 paired reads abnormally mapped. this method was implemented in the soapsv., we identified cnvs according to the mapping depth described previously. assuming a poisson’s distribution of sequencing depth, the genome regions were divided into initial windows, […]

2012
PMCID: 5520836
PMID: 27234240
DOI: 10.1186/1939-8433-5-18

[…] of 13× coverage was achieved (table ), and the resulting consensus sequence covered approximately 82.57% of the reference genome.table 1, 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 ). […]


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

SOAPsv in publications

 (15)
PMCID: 5928663
PMID: 29568937
DOI: 10.3892/mmr.2018.8773

[…] was removed and the purification data analyzed by sequence alignment. soap software (soapdenovo v2.04; soap3/gpu v0.01beta; soapaligner/soap2 v2.20; soapsplice v1.1; soapsnp v1.03; soapindel v1.0; soapsv v1.02) was used to analyze copy number, single nucleotide polymorphism (snp), and insertion/deletion (indel). annotations were used to screen suspected pathogenic variants. the polymorphism […]

PMCID: 5913671
PMID: 29420738
DOI: 10.1093/molbev/msy017

[…] each species was determined using soapsnp v1.04 with the criteria previously reported (). small insertions and deletions were identified using soapindel v2 (), and inversions and duplications using soapsv ()., to identify splice junctions, we first aligned the filtered rna-seq reads for each falcon to the falcon reference genome using bowtie 0.12.7. splice junctions were then predicted using […]

PMCID: 5937475
PMID: 29740511
DOI: 10.7717/peerj.4625

[…] pairs of reads were required to define an indel. for indels annotation, analysis of regional information and impact of indels on cds region, such as in a frameshift mutation, was possible., the soapsv (http://soap.genomics.org.cn/soapsv.html) program was used to detect structural variations by whole genome de novo assembly system requirements. structural variations (svs) is one […]

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

[…] the average contig size was 49 339 ± 6088 bps., we here applied an integrative strategy to identify the svs of han chinese people, including multiple current algorithms. the assembly-based method (soapsv) [] was firstly employed in sv calling. we finally obtained a total of 26 142 svs, containing 12 772 insertions and 13 370 deletions. the average number for each individual is 3102 ± 190. […]

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

[…] sequence data were uniquely aligned to the reference longan genome. snps, indels, and sequence variations were identified using soapsnp (http://soap.genomics.org.cn/soapsnp.html), 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 […]


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

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.

SOAPsv reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review SOAPsv