Accurate DNA Base Caller
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چکیده
منابع مشابه
DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads
The MinION device by Oxford Nanopore produces very long reads (reads over 100 kBp were reported); however it suffers from high sequencing error rate. We present an open-source DNA base caller based on deep recurrent neural networks and show that the accuracy of base calling is much dependent on the underlying software and can be improved by considering modern machine learning methods. By employ...
متن کاملDNA sequencing reads and variants calling using mapping quality scores ( Supplementary Text )
In this supplement text, a letter in uppercase indicates a random variable, whereas a letter in lowercase represents a constant, a known value or a function. Let Σ = {‘A’,‘C’,‘G’,‘T’} be the alphabet of the four nucleotides. In sequencing, the true nucleotide is B ∈ Σ and the one estimated by base caller is B̂. The base error B is defined as: B = Pr{B̂ 6= B} and base quality QB is: QB = −c log B ...
متن کاملDna Sequences Base Calling by Phred: Error Pattern Analysis
PHRED is the most frequently used base caller algorithm in genome projects. An interesting point on PHRED utilization is the fact that a low score on some base may not actually correspond to a miscalling on that base, but it may stand for a putative error on the region around this base. In order to evaluate the efficiency of PHRED on base calling and base quality assigning, we have sequenced pU...
متن کاملAn adaptive decorrelation method removes Illumina DNA base-calling errors caused by crosstalk between adjacent clusters
Base-calling accuracy is crucial for high-throughput DNA sequencing and downstream analysis such as read mapping and genome assembly. Accordingly, we made an endeavor to reduce DNA sequencing errors of Illumina systems by correcting three kinds of crosstalk in the cluster intensity data. We discovered that signal crosstalk between adjacent clusters accounts for a large portion of sequencing err...
متن کاملGW-CALL: Accurate Genome-Wide Variant Caller
The main challenge in reliable variant calling using DNA reads is to extract information from reads mappable to multiple locations on the reference genome. Conventional approaches ignore these reads and rely on reads mappable uniquely to the reference genome. These approaches fail to perform satisfactorily in variant calling within repeat regions which are abundant in many species including hom...
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تاریخ انتشار 2016