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SOAPsplice specifications


Unique identifier OMICS_01251
Name SOAPsplice
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Version 1.10
Stability Stable
Maintained Yes


  • Primates
    • Homo sapiens




No version available


  • person_outline Siu-Ming Yiu
  • person_outline Zhiyu Peng

Additional information

Publication for SOAPsplice

SOAPsplice citations


Deciphering Transcriptome and Complex Alternative Splicing Transcripts in Mammary Gland Tissues from Cows Naturally Infected with Staphylococcus aureus Mastitis

PLoS One
PMCID: 4961362
PMID: 27459697
DOI: 10.1371/journal.pone.0159719

[…] We used SOAPsplice software with a default setting and RNA-Seq data to detect splice junctions and identify the potential AS patterns of genes (Fig B in ). SOAPsplice uses a novel approach comprising the foll […]


Implication of Long noncoding RNAs in the endothelial cell response to hypoxia revealed by RNA sequencing

Sci Rep
PMCID: 4827084
PMID: 27063004
DOI: 10.1038/srep24141

[…] For transcriptomic analyses, quality-score filtered sequences were aligned to the human genome assembly of Ensembl (GRCh37/ hg19, Feb 2009, Version 72) using the SoapSplice alignment software. The number of uniquely mapping reads was estimated for each sample by using HTSeq-Count. Gene expression read counts were used to identify differential expressed genes ( […]


Transcriptomic, proteomic and metabolic changes in Arabidopsis thaliana leaves after the onset of illumination

BMC Plant Biol
PMCID: 4750186
PMID: 26865323
DOI: 10.1186/s12870-016-0726-3

[…] of mappable reads that fell onto the genes; N is the total number of maptable reads in the experiment; L is the sum of the genes in base pairs).Alternative splicing transcripts were analyzed based on SOAPsplice software []. For novel transcripts which were not identified in the TAIR10.0 database, the assembled transcripts must meet the following three criteria: (i) the length of the transcript mus […]


MicroRNA 222 regulates muscle alternative splicing through Rbm24 during differentiation of skeletal muscle cells

PMCID: 4849150
PMID: 26844700
DOI: 10.1038/cddis.2016.10
call_split See protocol

[…] 81, Analysis of count data was performed using htseq-count (v0.5.3p9) and DESeq2 after reads were aligned to the mouse genome (mm10) using SOAPSplice. In brief, DESeq2 uses generalized linear models based in the negative binomial distribution. We built linear models using two different experiments and two conditions (miR-222 overexpressi […]


Survey of Programs Used to Detect Alternative Splicing Isoforms from Deep Sequencing Data In Silico

Biomed Res Int
PMCID: 4573434
PMID: 26421304
DOI: 10.1155/2015/831352

[…] ese factors on AS research was analyzed. Using RNA-seq data produced by the Illumina/Solexa sequencing platform as an example, we compared three common splice site prediction programs (HMMSplicer [], SOAPsplice, and TopHat []) under conditions of different depths and sequence read lengths. The performance of each type of software was evaluated under different conditions by comparing the number of […]


Identification of potential HIV restriction factors by combining evolutionary genomic signatures with functional analyses

PMCID: 4434878
PMID: 25980612
DOI: 10.1186/s12977-015-0165-5

[…] 0 mio read pairs were obtained for the samples. Sequencing reads were quality filtered before alignment using Cutadapt [] and PrInseq []. Cleaned sequencing reads were aligned to a build genome using SOAPsplice. Gene expression was assessed by determining the number of mapped reads per gene using HTSeq-count tool, followed by DESeq R package normalization. An additional normalization step taking i […]


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SOAPsplice institution(s)
Bioinformatics Center, Beijing Genomics Institute at Shenzhen, Shenzhen, China; Department of Computer Science, The University of Hong Kong, Hong Kong, China

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