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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

Versioning


No version available

Maintainers


  • person_outline SOAP3
  • person_outline Jun Wang

Publication for SOAPindel

SOAPindel citations

 (18)
library_books

IMSindel: An accurate intermediate size indel detection tool incorporating de novo assembly and gapped global local alignment with split read analysis

2018
Sci Rep
PMCID: 5884821
PMID: 29618752
DOI: 10.1038/s41598-018-23978-z

[…] els. They can mainly be classified into three approaches: (1) realignment based approach (GATK, Scalpel, SV-STAT), (2) split-read approach (PINDEL, Splitread, PRISM), and (3) local assembly approach (SOAPindel). Recently, hybrid approaches that integrate these approaches have also been developed, resulting in more sensitive indel discovery methods than these approaches independently (ScanIndel).He […]

library_books

Intraspecific comparative genomics of isolates of the Norway spruce pathogen (Heterobasidion parviporum) and identification of its potential virulence factors

2018
BMC Genomics
PMCID: 5870257
PMID: 29580224
DOI: 10.1186/s12864-018-4610-4

[…] sulting 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 by VelvetOptimis […]

call_split

Whole Genome Sequence of the 1,4 Dioxane Degrading Bacterium Mycobacterium dioxanotrophicus PH 06

2017
Genome Announc
PMCID: 5578833
PMID: 28860235
DOI: 10.1128/genomeA.00625-17
call_split See protocol

[…] ntig 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 ve […]

library_books

Genome sequencing and analysis of Talaromyces pinophilus provide insights into biotechnological applications

2017
Sci Rep
PMCID: 5428652
PMID: 28352091
DOI: 10.1038/s41598-017-00567-0

[…] reducing 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 of the incorrectne […]

library_books

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

2017
GigaScience
PMCID: 5467034
PMID: 28368449
DOI: 10.1093/gigascience/gix023

[…] teps, the resulting 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-join […]

library_books

Complete Genome Sequence of the Dairy Isolate Lactobacillus acidipiscis ACA DC 1533

2017
Genome Announc
PMCID: 5270707
PMID: 28126948
DOI: 10.1128/genomeA.01533-16

[…] ize) and one PacBio mate pair 5k/6k. To estimate the genome size, k-mer analysis was performed. Afterward, SOAPdenovo v2.04 software was employed to assemble the reads after filtering, while SOAPsnp, SOAPindel, and GATK were applied for error correction. Furthermore, whole-genome optical mapping generated at Microbion SRL (Verona, Italy) was used to validate the hybrid assembly (). The alignment o […]

Citations

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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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