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Nevertheless, other biases caused by the sequencing process, such as a GC-content dependent production of reads [20], could also have a substantial effect on the estimated gene expression levels and these are not considered here.
This analysis enabled the identification of erroneous insertions or deletions of bases in the genome information produced by the sequencing process, and it avoided identification of false-positive pseudogenes.
This truncates reads at the location of substitution errors produced by the sequencing process.
Each arrested DNA molecule produced by the sequencing process contains one single fluorochrome linked to the sequencing primer; hence the height of a discriminating-peak is proportional to the relative frequency of the corresponding marker in the DNA solution.
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The major shortcoming of such high-throughput sequencing - short reads that can be difficult to assemble - are being overcome by advances in the sequencing process itself and novel bioinformatic approaches explored in studies such as this.
This could be explained by artifacts generated during the sequencing process.
Sequence lengths may also be shortened by the microsatellites themselves, as the sequencing process cycles nucleotides one after another.
Similarly, the pyrosequencing technology of 454 Life Sciences (Margulies et al., 2005) promises massive parallelization of the sequencing process by the use of microchip sensors, improving the speed of Sanger sequencing by a factor of a few hundred.
Because minor types would probably be covered by the predominant type in the sequencing process, sequencing would probably have resulted in underestimation of infection with multiple types.
We expect that the whole repertoire of species present in the sample can be detected by increasing the performance of the sequencing process.
We then mimic the sequencing process by randomly generating paired-end reads with varying parameters including coverage ratio, insert length of the reads and standard deviation of the insert length.
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