SOAP pipeline

SOAP specifications


Unique identifier OMICS_00688
Alternative name Short Oligonucleotide Analysis Package
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Input format FASTA
Output format Tab-delimited text, SAM
Operating system Unix/Linux
Programming languages C, C++, Perl
Parallelization CUDA
Computer skills Advanced
Version 3.0
Stability Beta
Maintained Yes


  • GapCloser



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

Publication for Short Oligonucleotide Analysis Package

SOAP citations

PMCID: 5658400

[…] generated per long rna library and small rna library, respectively. the clean reads produced from the long rna libraries were first mapped to the homo sapiens rrna database using the soapaligner/soap2 short read alignment software, to remove the remaining rrna reads. the non-rrna reads were used to perform the transcriptome assembling and quantification. first, non-rrna reads were mapped […]

PMCID: 5259909

[…] a standard illumina shotgun library was constructed and sequenced using the illumina hiseq 2000 platform; this generated 8,355,450 clean reads totaling 752 mbp. these reads were assembled using the short oligonucleotide analysis package (soapdenovo v2.04) with all parameters set to default [21]. the final draft assembly contains 25 contigs in 8 scaffolds. final assembly was based on all clean […]

PMCID: 5054682

[…] genome sequence and gene profiles of p. aeruginosa pao1 (genbank accession number: ae004091). the software tophat37 was used to map mrna sequences to the genome, and subsequently the combination of soap2 program38 and cufflinks39 was used to calculate the expected fragments per kilobase of transcript per million fragments (fpkm) sequenced. finally, the differentially expressed transcripts […]

PMCID: 5012053

[…] for the bioinformatics analyses., in consideration of rrna pollution interference in the analysis, the clean reads were mapped to an rrna reference sequence using the short reads alignment software soap2 ( to remove the remaining rrna reads. the remaining reads were used for transcriptome assembly and quantification., the removed rrna reads were mapped […]

PMCID: 4750186

[…] to the arabidopsis col-0 (tair10.0) nuclear-encoded cds gene set, the mitochondria-encoded cds gene set and the chloroplast-encoded cds gene set, respectively. the alignment tool is soapaligner/soap2 (parameters: -m 0 -× 10,000 -s 40 -l 32 -v 5 -r 2 -p 6) [41]. the transcript abundance was estimated by the rpkm (reads per kilobase transcript per million reads) calculation for each gene […]

SOAP institution(s)
HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory & Department of Computer Science, University of Hong Kong, Hong Kong, China; School of Computer Science, National University of Defense Technology, Changsha, Hunan, China; BGI-Shenzhen, Shenzhen, Guangdong, China; Peking-Tsinghua Center for Life Sciences, Biodynamic Optical Imaging Center and School of Life Sciences, Peking University, Beijing, China; Department of Computer Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
SOAP funding source(s)
Supported by RGC General Research Fund 10612042, Hong Kong ITF Grant GHP/011/12 and the GRF Grant HKU-713512E.

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