SOAPindel protocols

SOAPindel specifications

Information


Unique identifier OMICS_00099
Name SOAPindel
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Biological technology Illumina, Roche
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainers


  • person_outline SOAP3 <>
  • person_outline Jun Wang <>
  • person_outline Mikkel Schierup <>

Publication for SOAPindel

SOAPindel IN pipelines

 (2)
2017
PMCID: 5734874
PMID: 29252184
DOI: 10.7554/eLife.27469.027

[…] short indels were determined using genome analysis toolkit (gatk) (mckenna et al., 2010; depristo et al., 2011; van der auwera et al., 2013), and we combined the output of several tools including soapindel, prism and pindel (li et al., 2013; jiang et al., 2012; ye et al., 2009) to increase the sensitivity of indels detection. we performed a stringent calling procedure for both snvs and indels […]

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

[…] to be supported by high quality data, and to minimize possible errors caused by repeated sequences., for short indels’ the ‘gaps allowed’ mapping result above was subjected to indel detection using soapindel (li et al., 2013), and gaps supported by more than one third of the mapped reads were retained as qualified indels. in this study, indels are defined as insertions or deletions of 5 bp […]

SOAPindel institution(s)
BGI Shenzhen, Shenzhen, China; Bioinformatics Research Centre, Aarhus University, Denmark; Broad Institute, Cambridge, MA, USA; Human Genetics, Aarhus University, Denmark; The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark; Department of Biology, University of Copenhagen, Copenhagen, Denmark
SOAPindel funding source(s)
Supported by EU FP7 Marie Curie IAPP ‘‘NextGene,’’ BGI-Shenzhen, LuCamp (Lundbeck Foundation Center), the Danish Research Councils, the National Basic Research Program of China (973 program no. 2011CB809201, 2011CB809202, 2011CB809203), the National Natural Science Foundation of China (30890032, 31161130357), Shenzhen Key Laboratory of Transomics Biotechnologies (CXB201108250096A), and Shenzhen Key Laboratory of Gene Bank for National Life Science.

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