SOAP: short oligonucleotide alignment program

By Ruiqiang Li, Yingrui Li, Karsten Kristiansen, Jun Wang. Bioinform., 2008

3,419 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/961fc29e45772c74b53f56b77bc44f0620eccd64

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

In Molecular Biology

Citations in the corpus

The impact of next-generation sequencing on genomics (2011, methodology): “Benchmarks comparing ELAND with other popular NGS software, such as MAQ, BLAST (Basic Local Alignment Search Tool), SOAP (Short Oligonucleotide Alignment Program) (Li et al., 2008b), and SeqMap (Jiang and Wong, 2008), etc. (Table 3), generally place ELAND as one of the fastest available programs.”
The genome of Theobroma cacao (2011, neutral): “Cacao chromosome Arabidopsis chromosome C1(1321) A1(63)-A2(85)-A3(69)-A4(116)-A5(64) C2(935) A1(89)-A2(30)-A4(61)-A5(10) C3(1018) A1(70)-A3(17)-A4(63)-A5(130) C4(837) A1(21)-A2(9)-A3(94)-A4(36)-A5(44) C5(820) A1(24)-A2(51)-A3(78)-A5(37) C6(616) A1(59)-A2(15)-A4(66)-A5(26) C7(287) A1(5)-A5(32) C8(605”
PeakSeq: Systematic Scoring of ChIP-Seq Experiments Relative to Controls (2009, neutral): “Xuan, Cold Spring Harbor Laboratories, personal communication), SOA”
BSMAP: whole genome bisulfite sequence MAPping program (2009, positive): “We implemented BSMAP based on the open source software SOAP (Short Oligonucleotide Alignment Program) [5].”
Next-generation sequencing: from basic research to diagnostics. (2009, methodology): “Software packages available for alignment and assembly to a reference sequence include Zoom (71) ,M AQ(67), Mosaik (72), SOAP ( 73 ), and SHRiMP (http://compbio.cs.toronto.edu/shrimp/), which supports SOLiD color-space analysis.”
MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping (2013, methodology): “…hashes to the reference genome, while MOM (Eaves and Gao 2009), MOSAIK, PASS (Campagna et al. 2009), ProbeMatch (Kim et al. 2009), SOAP (Ruiqiang Li et al. 2008), SRmapper (Gontarz et al. 2013), and STAMPY (Lunter and Goodson 2011) hash the reference genome and store this for comparison with…”
Estimating accuracy of RNA-Seq and microarrays with proteomics (2009, positive): “To map the resulting 36-nucleotide long sequencing reads to the human genes, we aligned all the reads against the whole genome (hg18) and all the transcripts downloaded from Ensembl database using the SOAP algorithm [30].”
Genome-wide Methylation Profiles Reveal Quantitative Views of Human Aging Rates (2012, positive): “Genotype calls were made with the SOAP program (Li et al., 2008).”
RNA-Seq: a revolutionary tool for transcriptomics (2009, methodology): “There are several programs for mapping reads to the genome, including ELAND, SOA”