SOAP protocols

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SOAP specifications

Information


Unique identifier OMICS_00688
Name SOAP
Alternative name Short Oligonucleotide Analysis Package
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format FASTA
Output format Tab-delimited text, SAM
Operating system Unix/Linux
Programming languages C++, Perl
Parallelization CUDA
Computer skills Advanced
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Short_Oligonucleotide_Analysis_Package

Subtool


  • GapCloser

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Maintainers


  • person_outline SOAP3 <>
  • person_outline Tak-Wah Lam <>
  • person_outline Yingrui Li <>
  • person_outline Ruiqiang Li <>

Publication for Short Oligonucleotide Analysis Package

SOAP in pipelines

 (25)
2018
PMCID: 5892942
PMID: 29570727
DOI: 10.1371/journal.ppat.1006942

[…] checked by fastqc []. mirtools2.0 [] pipeline is used for trimming (“adaptor_trim.pl” script) and downstream analysis of known mirnas. sequencing reads are aligned to the bostau7 genome using soap []. annotations are added from mirbase 21 [] and rfam [] databases. the differential expression of each known mirnas from their absolute read counts are analysed by deseq2 []. differential […]

2018
PMCID: 5904165
PMID: 29666397
DOI: 10.1038/s41598-018-24443-7

[…] of c. neopsychrotolerans sl-16 was extracted using the ctab method. the 500-bp insert library was sequenced using the illumina pe250 system. the clean reads were then assembled by soapdenovo (http://soap.genomics.org.cn, v2.04) for data processing. genes were subsequently predicted using augustus 3.2.1 and genemark-es 4.21 with default parameters, which were further integrated by the glean […]

2017
PMCID: 5660214
PMID: 29079830
DOI: 10.1038/s41598-017-14738-6

[…] from ncbi (srr555564) and assembled into unigenes using the trinity 2.4.0 software. the snp-associated rad tag sequences were aligned against the assembled transcriptome of a. konjac using soap 2.21 with the default settings. to investigate the gene function of loci, a blastx search was applied against ncbi’s non-redundant database by blast 2.2.28 with an e-value of 1e−6. according […]

2016
PMCID: 5067666
PMID: 26857916
DOI: 10.1111/pbi.12533

[…] rnas were used for further analysis. high‐quality clean small rna tags were mapped to tomato genome (ftp://ftp.solgenomics.net/tomato_genome/annotation/itag2.4_release/itag2.4_genomic.fasta) by soap (short oligonucleotide alignment program) to find out their expression and distribution on the genome (li et al., ). then, the matched tags were aligned to ncbi genbank […]

2016
PMCID: 5084871
PMID: 27789647
DOI: 10.1128/genomeA.01215-16

[…] dna was sequenced using an illumina hiseq 2000 sequencing platform (illumina, ca, usa). a total of 1,463 mb data was produced and the short reads were assembled into a genome sequence using the soap de novo method (). the total length of the draft genome was 4,077,699 bp with a mean g+c content of 35.7%. the assembly contained 26 scaffolds and 27 contigs. gene prediction was performed […]


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SOAP in publications

 (209)
PMCID: 5946483
PMID: 29747580
DOI: 10.1186/s12864-018-4739-1

[…] with an insertion size of 500 bp, 2 kb, and 6 kb, respectively. low-quality reads were filtered by trimmomatic []. the high-quality reads were used for de novo assembly and scaffolding using soap denovo (version 1.05, http://soap.genomics.org.cn/soapdenovo.html). gaps closure was performed using gapcloser v1.12 [, ]. the completeness of the c. pseudoreteaudii genome was evaluated using […]

PMCID: 5930818
PMID: 29716635
DOI: 10.1186/s12977-018-0417-2

[…] the most commonly used mapping algorithms used for this task include bowtie [], bowtie2 [], star [], novoalign (http://www.novocraft.com/products/novoalign/), rmap [], tophat [], gsnap [], soap [] and bwa [], some with unique advantages over others depending on whether mapping is done on a genome versus transcriptome. the choice of algorithm and the parameters for mapping will need […]

PMCID: 5904165
PMID: 29666397
DOI: 10.1038/s41598-018-24443-7

[…] of c. neopsychrotolerans sl-16 was extracted using the ctab method. the 500-bp insert library was sequenced using the illumina pe250 system. the clean reads were then assembled by soapdenovo (http://soap.genomics.org.cn, v2.04) for data processing. genes were subsequently predicted using augustus 3.2.1 and genemark-es 4.21 with default parameters, which were further integrated by the glean […]

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

[…] to obtain double terminal sequence of 90 bp reads. for the removal of the low-quality and polluted 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 […]

PMCID: 5797411
PMID: 29434667
DOI: 10.1186/s13068-018-1015-1

[…] proteins was predicted by the protcomp 9.0 program (for animals and fungi, http://www.softberry.com)., to quantify the expression of unigenes, reads were mapped to the unigene sequence using a soap aligner allowing a maximum of three mismatches in one read []. an in-house perl script was used to count the number of reads that mapped to each unigene. only the reads that uniquely mapped […]


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SOAP institution(s)
Beijing Genomics Institute at Shenzhen, Shenzhen, China; Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
SOAP funding source(s)
Supported by the National Natural Science Foundation of China (30725008), and grants from the Danish Natural Science Research Council (272-05- 0344 and 272-07-0196).

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