{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,31]],"date-time":"2025-10-31T14:02:10Z","timestamp":1761919330570},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2315,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: High-throughput sequencing (HTS) technologies are transforming the study of genomic variation. The various HTS technologies have different sequencing biases and error rates, and while most HTS technologies sequence the residues of the genome directly, generating base calls for each position, the Applied Biosystem's SOLiD platform generates dibase-coded (color space) sequences. While combining data from the various platforms should increase the accuracy of variation detection, to date there are only a few tools that can identify variants from color space data, and none that can analyze color space and regular (letter space) data together.<\/jats:p>\n               <jats:p>Results: We present VARiD\u2014a probabilistic method for variation detection from both letter- and color-space reads simultaneously. VARiD is based on a hidden Markov model and uses the forward-backward algorithm to accurately identify heterozygous, homozygous and tri-allelic SNPs, as well as micro-indels. Our analysis shows that VARiD performs better than the AB SOLiD toolset at detecting variants from color-space data alone, and improves the calls dramatically when letter- and color-space reads are combined.<\/jats:p>\n               <jats:p>Availability: The toolset is freely available at http:\/\/compbio.cs.utoronto.ca\/varid<\/jats:p>\n               <jats:p>Contact: \u00a0varid@cs.toronto.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq184","type":"journal-article","created":{"date-parts":[[2010,6,7]],"date-time":"2010-06-07T07:28:13Z","timestamp":1275895693000},"page":"i343-i349","source":"Crossref","is-referenced-by-count":9,"title":["VARiD: A variation detection framework for color-space and letter-space platforms"],"prefix":"10.1093","volume":"26","author":[{"given":"Adrian V.","family":"Dalca","sequence":"first","affiliation":[{"name":"1 Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA, 2 Department of Computer Science, University of Toronto, Toronto, ON, Canada, 3 Department of Computer Science, Stanford University, Stanford , 4 Scripps Genomic Medicine, The Scripps Research Institute, La Jolla, CA, USA and 5 Donnelly Centre and the Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada"},{"name":"1 Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA, 2 Department of Computer Science, University of Toronto, Toronto, ON, Canada, 3 Department of Computer Science, Stanford University, Stanford , 4 Scripps Genomic Medicine, The Scripps Research Institute, La Jolla, CA, USA and 5 Donnelly Centre and the Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada"}]},{"given":"Stephen M.","family":"Rumble","sequence":"additional","affiliation":[{"name":"1 Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA, 2 Department of Computer Science, University of Toronto, Toronto, ON, Canada, 3 Department of Computer Science, Stanford University, Stanford , 4 Scripps Genomic Medicine, The Scripps Research Institute, La Jolla, CA, USA and 5 Donnelly Centre and the Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada"}]},{"given":"Samuel","family":"Levy","sequence":"additional","affiliation":[{"name":"1 Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA, 2 Department of Computer Science, University of Toronto, Toronto, ON, Canada, 3 Department of Computer Science, Stanford University, Stanford , 4 Scripps Genomic Medicine, The Scripps Research Institute, La Jolla, CA, USA and 5 Donnelly Centre and the Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada"}]},{"given":"Michael","family":"Brudno","sequence":"additional","affiliation":[{"name":"1 Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA, 2 Department of Computer Science, University of Toronto, Toronto, ON, Canada, 3 Department of Computer Science, Stanford University, Stanford , 4 Scripps Genomic Medicine, The Scripps Research Institute, La Jolla, CA, USA and 5 Donnelly Centre and the Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada"},{"name":"1 Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA, 2 Department of Computer Science, University of Toronto, Toronto, ON, Canada, 3 Department of Computer Science, Stanford University, Stanford , 4 Scripps Genomic Medicine, The Scripps Research Institute, La Jolla, CA, USA and 5 Donnelly Centre and the Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada"}]}],"member":"286","published-online":{"date-parts":[[2010,6,1]]},"reference":[{"key":"2023012508083818000_B1","doi-asserted-by":"crossref","first-page":"967","DOI":"10.1093\/bioinformatics\/btp087","article-title":"Pass: a program to align short sequences","volume":"25","author":"Campagna","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012508083818000_B2","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1093\/bib\/bbp058","article-title":"Genome variation discovery with high-throughput sequencing data","volume":"11","author":"Dalca","year":"2010","journal-title":"Brief Bioinform."},{"key":"2023012508083818000_B3","volume-title":"Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids.","author":"Durbin","year":"1999"},{"issue":"Suppl.11","key":"2023012508083818000_B4","doi-asserted-by":"crossref","first-page":"S6","DOI":"10.1038\/nmeth.1376","article-title":"Sense from sequence reads: methods for alignment and assembly","volume":"6","author":"Flicek","year":"2009","journal-title":"Nat. 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