SOAPsnp protocols

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SOAPsnp statistics

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SOAPsnp specifications

Information


Unique identifier OMICS_00078
Name SOAPsnp
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for SOAPsnp

SOAPsnp in pipelines

 (40)
2018
PMCID: 5894961
PMID: 29641573
DOI: 10.1371/journal.pone.0185237

[…] in . the reference was obtained from the ncbi, version grch37 (hg19). sequence alignment was performed using burrows wheeler aligner (bwa) multi-vision software package []. snvs were called by soapsnp [] and small indels (<20bp) were identified using the samtools (tools for alignments in the sam format) version: 0.1.18, http://samtools.sourceforge.net/., the screening method of copy […]

2017
PMCID: 5339403
PMID: 28161492
DOI: 10.1016/j.gpb.2016.11.001

[…] provided in trinity , ., the unigenes assembled from trinity was used as the reference genome for snp discovery. reads from the b. hookeriana samples were mapped onto the reference using soapsnp (with parameters -u t -q i -l 90) to detect the snp . soapsnp calculates the likelihood of each genotype at each site and then infers the genotype using highest posterior probability […]

2017
PMCID: 5341019
PMID: 28272483
DOI: 10.1038/srep43939

[…] command bwa-mem). sequence alignment/map (sam) format alignment result files were imported to samtools and the ‘rmdup’ command was used to remove potential pcr duplicates. snps were detected by soapsnp and annotated with annovar. snps with minor allele frequencies (maf) less than 0.05 and deviated from hardy-weinberg equilibrium (p < 0.001) were excluded. haploview was used to select tag […]

2017
PMCID: 5400587
PMID: 28423518
DOI: 10.18632/oncotarget.15570

[…] region and sequencing depth computation, snp and indel calling, and cnv detection. first, a novel three-step computational frame work for cnv was applied. then, snps and indels were called using soapsnp software and sam tools pileup software, respectively. a snp or indel was be filtered if it could not follow the criterion: supported by at least 10 reads and > 20% of the total reads. […]

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

[…] or 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 […]


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SOAPsnp in publications

 (274)
PMCID: 5920022
PMID: 29731767
DOI: 10.3389/fgene.2018.00129

[…] reference genome (hg19) with maximum 3 mismatches, the parameters were set as ‘-a -b -d -o -u -2 -t -v 3 -l 35 -s 40 -m 0 -x 500 -p 4 -r 1 -n 0’. based on the results from soapaligner, software soapsnp (v1.05) was used to assemble the consensus sequence and call genotypes in target regions. the following parameters were set: -q k -i -d -o -r 0.0005 -e 0.001 -u -l 90 -t -s -2,where ‘-t’ used […]

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

[…] least 1000 bp. the resulting 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 […]

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

[…] reads, the 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 […]

PMCID: 5842585
PMID: 29514627
DOI: 10.1186/s12881-018-0549-1

[…] was used for library preparation, and a nimblegen sequence capture array was used for sequence capture. illumina pipeline software (version 1.3.4) was used to analyze the primary sequencing data. soapsnp software and sam tools pileup software were used to analyze the gene mutations., to confirm the wrap53 arg298trp mutation identified by ngs, the corresponding wrap53 gene region surrounding […]

PMCID: 5840468
PMID: 29531467
DOI: 10.3748/wjg.v24.i9.1035

[…] 3′-/5′- adapters and low-quality reads, respectively. clean short reads were mapped to the human genome (hg19) using burrows wheeler aligner software (http://sourceforge.net/projects/bio-bwa/). soapsnp software (http: //soap.genomics.org.cn/) and sam tools pileup software (http://sourceforge.net/projects/samtools/) were used to detect single-nucleotide polymorphisms and small insertions […]


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SOAPsnp institution(s)
Beijing Genomics Institute at Shenzhen, Shenzhen, China

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