SOAP: Short oligonucleotide alignment program
Open accessAbstract
Summary: We have developed a program SOAP for efficient gapped and ungapped alignment of short oligonucleotides onto reference sequences. The program is designed to handle the huge amounts of short reads generated by parallel sequencing using the new generation Illumina-Solexa sequencing technology. SOAP is compatible with numerous applications, including single-read or pair-end resequencing, small RNA discovery and mRNA tag sequence mapping. SOAP is a command-driven program, which supports multi-threaded parallel computing, and has a batch module for multiple query sets. Availability: http://soap.genomics.org.cn Contact: soap@genomics.org.cn
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SOAP is particularly efficient in handling throughput sequencing data, making it a popular choice for SNP discovery and genotyping analyses.
“It is particularly efficient in handling throughput sequencing data, making it a popular choice for SNP discovery and genotyping analyses (Figure 10).”
From Whole-Genome Alignment: Methods, Challenges, and Future Directions (2024) · cites this paper as [51]
The Abstract says SOAP was designed for large volumes of short sequencing reads, and the performance comparison reports that it aligned nearly 10 million reads much faster than BLASTN. The paper discusses resequencing for studies of genetic variation, but our copy does not establish that SOAP was a popular choice specifically for SNP discovery or genotyping. (LLM, conf=0.85)
Experimental — accuracy not yet measuredSOAP uses a straightforward hashing strategy to align short reads against a reference genome.
“SOAP (short oligonucleotide alignment program) uses a straightforward hashing strategy to align short reads against a reference genome [51].”
From Whole-Genome Alignment: Methods, Challenges, and Future Directions (2024) · cites this paper as [51]
SOAP typically has a worst-case time complexity of O(n^2), where n is the length of the input sequences.
“It typically has a worst-case time complexity of O ( n 2 ), where n is the length of the input sequences;”
From Whole-Genome Alignment: Methods, Challenges, and Future Directions (2024) · cites this paper as [51]
Our copy describes SOAP’s seed-and-hash alignment method and reports measured runtimes in Table 1 (both indexed under Abstract, with no page given). It does not state a worst-case time complexity of O(n²) or define such a bound in terms of input-sequence length; searches for those terms found no supporting passage. (LLM, conf=0.75)
Experimental — accuracy not yet measured
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- Authors
- Li, R., Li, Y., Kristiansen, K., & Wang, J.
- Affiliations
- BGI Group (China) (CN)
- Corresponding author
- Wang, Jun
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2008-01-28
- Volume
- 24
- Issue
- 5
- Pages
- 713-714
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2139760555
- Cited by
- 3,597
- References
- 1
- Citations by year
- 2026: 272 · 2025: 289 · 2024: 303 · 2023: 254 · 2022: 254 · 2021: 263 · 2020: 191 · 2019: 172 · 2018: 140 · 2017: 145 · 2016: 149 · 2015: 199 · 2014: 196 · 2013: 196 · 2012: 179
- FWCI
- 50.02
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- University of Southern Denmark Research Portal (University of Southern Denmark) (submittedVersion)
- Funders
- National Natural Science Foundation of China (30725008)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Computer Science › Artificial Intelligence › Algorithms and Data Compression
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
- Keywords
- soap, gapped alignment, short read mapping, Illumina sequencing, resequencing, batch processing
- MeSH terms
- Sequence Alignment, Sequence Homology, Amino Acid, Sequence Analysis, DNA
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