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Availability of reliable simulated dataset is essential and is the first step towards testing any newly developed analytical tools for variant discovery. Although there are tools currently available that can simulate variants, none present the possibility of simulating all the three major types of variations (Single Nucleotide Polymorphisms, Insertions and Deletions and Copy Number Variations) and can generate reads taking a realistic error-model into consideration. Therefore, an efficient simulator and read generator is needed that can simulate variants taking the error rates of true biological samples into consideration.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We report SInC (<jats:bold>S<\/jats:bold>np, <jats:bold>In<\/jats:bold>del and <jats:bold>C<\/jats:bold>nv) an open-source variant simulator and read generator capable of simulating all the three common types of biological variants taking into account a distribution of base quality score from a most commonly used next-generation sequencing instrument from Illumina. SInC is capable of generating single- and paired-end reads with user-defined insert size and with high efficiency compared to the other existing tools. SInC, due to its multi-threaded capability during read generation, has a low time footprint. SInC is currently optimised to work in limited infrastructure setup and can efficiently exploit the commonly used quad-core desktop architecture to simulate short sequence reads with deep coverage for large genomes.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>We have come up with a user-friendly multi-variant simulator and read-generator tools called SInC. SInC can be downloaded from <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/sourceforge.net\/projects\/sincsimulator\" ext-link-type=\"uri\">http:\/\/sourceforge.net\/projects\/sincsimulator<\/jats:ext-link>.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-15-40","type":"journal-article","created":{"date-parts":[[2014,2,5]],"date-time":"2014-02-05T06:02:02Z","timestamp":1391580122000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":60,"title":["SInC: an accurate and fast error-model based simulator for SNPs, Indels and CNVs coupled with a read generator for short-read sequence data"],"prefix":"10.1186","volume":"15","author":[{"given":"Swetansu","family":"Pattnaik","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Saurabh","family":"Gupta","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arjun A","family":"Rao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Binay","family":"Panda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2014,2,5]]},"reference":[{"issue":"2","key":"6307_CR1","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1007\/s10555-011-9278-z","volume":"30","author":"MR Schweiger","year":"2011","unstructured":"Schweiger MR, Kerick M, Timmermann B, Isau M: The power of NGS technologies to delineate the genome organization in cancer: from mutations to structural variations and epigenetic alterations. 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