SOAPsv protocols

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


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Maintainers


  • person_outline SOAP3 <>
  • person_outline Jian Wang <>

Publication for SOAPsv

SOAPsv IN pipelines

 (3)
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

[…] reference and unmapped reads. average sequencing depth and coverage were calculated using the alignment results.20 the mapped reads were then used to detect snps, indels, and svs using soapsnp and soapsv software with default parameter settings.20–22 the snps identified were filtered based on the following stringent criteria: no less than two times for coverage depth (no less than three times […]

2012
PMCID: 3285608
PMID: 22383984
DOI: 10.1371/journal.pone.0030952

[…] 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 [14], yielding 267,383 snps from the genome of ir24, 288,764 snps from that of mh63, and 259,862 snps from that of sh527 (table 3, […]

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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