{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T18:28:27Z","timestamp":1788200907071,"version":"build-2803163510"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>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.<\/jats:p>\n                  <jats:p>Availability: \u00a0http:\/\/soap.genomics.org.cn<\/jats:p>\n                  <jats:p>Contact: \u00a0soap@genomics.org.cn<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn025","type":"journal-article","created":{"date-parts":[[2008,1,28]],"date-time":"2008-01-28T20:34:06Z","timestamp":1201552446000},"page":"713-714","source":"Crossref","is-referenced-by-count":3147,"title":["SOAP: short oligonucleotide alignment program"],"prefix":"10.1093","volume":"24","author":[{"given":"Ruiqiang","family":"Li","sequence":"first","affiliation":[{"name":"1 Beijing Genomics Institute at Shenzhen, Shenzhen 518083, China and 2Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, DK-5230, Denmark"},{"name":"1 Beijing Genomics Institute at Shenzhen, Shenzhen 518083, China and 2Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, DK-5230, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yingrui","family":"Li","sequence":"additional","affiliation":[{"name":"1 Beijing Genomics Institute at Shenzhen, Shenzhen 518083, China and 2Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, DK-5230, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karsten","family":"Kristiansen","sequence":"additional","affiliation":[{"name":"1 Beijing Genomics Institute at Shenzhen, Shenzhen 518083, China and 2Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, DK-5230, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun","family":"Wang","sequence":"additional","affiliation":[{"name":"1 Beijing Genomics Institute at Shenzhen, Shenzhen 518083, China and 2Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, DK-5230, Denmark"},{"name":"1 Beijing Genomics Institute at Shenzhen, Shenzhen 518083, China and 2Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, DK-5230, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2008,1,28]]},"reference":[{"key":"2023020210120433100_B1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"2023020210120433100_B2","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1016\/j.gde.2006.10.009","article-title":"Whole-genome re-sequencing","volume":"16","author":"Bentley","year":"2006","journal-title":"Curr. 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