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This is supported by our previous findings where Acinetobacter and Pseudomonas spp. were detected on Pangasius samples collected at the filleting and trimming steps of processing in Vietnamese companies (Tong Thi et al. 2013).
Unpaired-end reads resulting from the previous trimming steps were discarded.
Of the total of 5 300 ESTs, 770 were removed during the quality trimming steps.
These trimming steps were achieved using internal software based on the FastX package [ 29].
A series of filtering and trimming steps were undertaken to remove low quality reads and bases using the prinseq-lite software [ 27] (trim_qual_right 28, trim_qual_type mean, trim_qual_window 5).
As part of the 'alignment trimming' steps a core sequence was chosen to improve the quality of the multiple sequence alignment but also assist the primer design.
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The trimming step is performed in situ as part of the polysilicon gate etching process.
The total number of reads passing the trimming step was 116,899 (84.9%).
For detail summary of the trimming step statistics refer to Table 1.
A summary of the trimming step statistics is reported in Table 1.
Spurs are a common form of noise, and not all spurs would be corrected during the overlap-based trimming step.
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