title: SOAP: short oligonucleotide alignment program.
abstract: CONCLUSIONS
  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.
  
  
  BACKGROUND
  http://soap.genomics.org.cn.
authors.affiliation: Beijing Genomics Institute at Shenzhen, Shenzhen 518083, China.
authors.forename: Ruiqiang
authors.initials: R
authors.lastname: Li
authors.forename: Yingrui
authors.initials: Y
authors.lastname: Li
authors.forename: Karsten
authors.initials: K
authors.lastname: Kristiansen
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
mesh_terms: D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid