SOAPindel protocols

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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 <>

Publication for SOAPindel

SOAPindel in pipelines

 (6)
2017
PMCID: 5428652
PMID: 28352091
DOI: 10.1038/s41598-017-00567-0

[…] as many captured gaps as possible using software pbjelly. to improve the accuracy of the genome sequences, gatk (https://www.broadinstitute.org/gatk/) and soap tool packages (soap2, soapsnp, soapindel), were used to make single-base corrections., a dna library of 500 bp inserts was constructed and pe sequenced. for generated hiseq reads, q20, representing the probability […]

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

[…] that was experimentally validated (see material and methods). snvs and short indels were determined using genome analysis toolkit (gatk) (; ; ), and we combined the output of several tools including soapindel, prism and pindel (; ; ) to increase the sensitivity of indels detection. we performed a stringent calling procedure for both snvs and indels and we only considered variants […]

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

[…] this value is higher than those observed in our targeted experiments, but lower than in cycling cells. among the 77 indels, all the events detected with gatk were found as well with either pindel, soapindel or prism (; ; ). among these indels, 26 are deletions (25/77–35%), a value two times greater than reported in ma lines of cycling cells (14%–17%) (; ). consistent with what was observed […]

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 (), 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 or less in length, […]

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

[…] using soapaligner with a parameter “–g 10”, which allows maximum of 10 bp gap within the hit of one single read. small insertions and deletions (1–10 bp), referred as indels, were identified using soapindel. for identification of svs, we used the pair-end mapping information for identifying reads with abnormal insert sizes, or only one end mapped to the genome and determined a sv […]


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SOAPindel in publications

 (30)
PMCID: 5870257
PMID: 29580224
DOI: 10.1186/s12864-018-4610-4

[…] subreads were self-corrected by falcon genome assembly tool kit v.0.3.0 and assembled into contigs by celera assembler v.8.3 [] followed by single base corrections using soapsnp v.1.05 [] and soapindel v.1.08 [] pipelines with hiseq pe reads. scaffolding was performed by sspace- longread [] using hiseq mp reads., filtered reads of re-sequenced isolates were assembled de novo […]

PMCID: 5928663
PMID: 29568937
DOI: 10.3892/mmr.2018.8773

[…] adapter sequence 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. […]

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

[…] genomes (ensembl 83) using soap v2.21. snp calling of 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 […]

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

[…] snps could correspond to a homologous functional element region, such as coding sequence (cds) region, exon region, utr region and others. this information could help us to select desired snps., soapindel software was designed for all paired-end sequencing data, wherein soapindel comparison allowed open gaps, and short insertions or deletion (indel) detections was performed. during short […]

PMCID: 5578833
PMID: 28860235
DOI: 10.1128/genomeA.00625-17

[…] with a length close to the estimated genome size, and illumina reads were used to correct and optimize the assembly results. third, the contig’s bases were corrected with quiver, pilon, soapsnp, soapindel (http://soap.genomics.org.cn), and gatk (http://www.broadinstitute.org/gatk). fourth, contig circle analysis was completed by verifying overlap regions. fifth, glimmer (), trf (), rnammer […]


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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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