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Specification deals with the representation and assignment of quality attribute properties of individual system elements to features.
Base call conversion and assignment of quality scores was performed using Illumina's CASAVA_v1.7 software.
VarScan is therefore reliant on accurate assignment of quality scores during the sequencing platform's base calling pipeline.
Furthermore, the input template supports the assignment of quality parameters (e. g. confidence interval) to each flux measurement value.
Phred (Ewing et al., 1998) is responsible for the base calls and the assignment of quality scores.
The proprietary genome analyzer software was used for the first preprocessing of sequence reads including the assignment of quality scores to generate.sff-files for further processing and assembly of the data.
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PHRED software [ 65] was used for base calling and assignment of base quality values, and vector and low quality-sequences were removed from the reads on the Egene platform [ 66].
The description of the sequencing, alignment, and assignment of estimated quality scores is described in Langley et al. (2012).
Data obtained from participants' use of the comparator instrument was analyzed to determine if using the comparator instrument resulted in the same assignment of overall quality of each article as was found with the new appraisal instrument.
The stringent approach taken here with orthology assignment of high quality contigs and rigorous trimming of the resultant alignments is therefore rather conservative, despite a considerable loss of data.
The analysis of NGS data is commonly based on three main analytic steps [ 164, 165], which are usually implemented via specific bioinformatic tools: (i) generation of sequences and assignment of base quality scores; (ii) demultiplexing (if necessary), read alignment, and variant calling; and (iii) identification and interpretation of variants according to guidelines [ 166].
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