Quality-score guided error correction for short-read sequencing data using CUDA
نویسندگان
چکیده
منابع مشابه
SHREC: a short-read error correction method
MOTIVATION Second-generation sequencing technologies produce a massive amount of short reads in a single experiment. However, sequencing errors can cause major problems when using this approach for de novo sequencing applications. Moreover, existing error correction methods have been designed and optimized for shotgun sequencing. Therefore, there is an urgent need for the design of fast and acc...
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MOTIVATION Error correction is critical to the success of next-generation sequencing applications, such as resequencing and de novo genome sequencing. It is especially important for high-throughput short-read sequencing, where reads are much shorter and more abundant, and errors more frequent than in traditional Sanger sequencing. Processing massive numbers of short reads with existing error co...
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Developing accurate, scalable algorithms to improve data quality is an important computational challenge associated with recent advances in high-throughput sequencing technology. In this study, a novel error-correction algorithm, called ECHO, is introduced for correcting base-call errors in short-reads, without the need of a reference genome. Unlike most previous methods, ECHO does not require ...
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BACKGROUND Different high-throughput nucleic acid sequencing platforms are currently available but a trade-off currently exists between the cost and number of reads that can be generated versus the read length that can be achieved. METHODOLOGY/PRINCIPAL FINDINGS We describe an experimental and computational pipeline yielding millions of reads that can exceed 200 bp with quality scores approac...
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Motivation Next-generation sequencing platforms have produced huge amounts of sequence data. This is revolutionizing every aspect of genetic and genomic research. However, these sequence datasets contain quite a number of machine-induced errors-e.g. errors due to substitution can be as high as 2.5%. Existing error-correction methods are still far from perfect. In fact, more errors are sometimes...
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ژورنال
عنوان ژورنال: Procedia Computer Science
سال: 2010
ISSN: 1877-0509
DOI: 10.1016/j.procs.2010.04.125