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The decision to retain the violent acts in the inventory was based on whether they achieved a minimum average score of 5. Step 4 (pretest).
To meet our sequence quality criteria, the resulting clone consensus sequence was required to achieve a minimum average score of Phred35, with each base position having a minimum score of Phred30.
To meet our hq criteria, the resulting clone consensus sequence was required to achieve a minimum average score of Phred35, with each base position having a minimum score of Phred30.
Empirical articles achieving a minimum average score of 10 (of a possible 17) and non-empirical and grey articles scoring a minimum of 5 (of a possible 10; see Additional file 3 for quality rating sheets) were retained.
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First, reads were quality filtered on read length (200 450 bp) allowing for homopolymers (maximum 8), a maximum of 2 differences with the primer sequence and minimum average quality score of 20 over a window of 50 base pairs.
In addition, the assembled contig should have a minimum average QV score of 40 and >50% overlap in the alignment of the forward and reverse reads.
Previous results obtained in a smaller pilot study [17] indicated that a minimum average quality score of 12 was an acceptable threshold, and, therefore, all sequence reads with an average quality score<12 were removed from the dataset.
Parameters for SNP detection included: a minimum read coverage at the potential SNP of 6, window length of 9, minimum average quality score of 15 and minimum central quality (i.e. quality of the SNP base) of 20.
Using the 454 base quality scores, which range from 0 40 (0 being an ambiguous base), sequences were trimmed using a sliding-window technique, such that the minimum average quality score over a window of 50 bases never dropped below 30.
Quality scores (Q) were calculated based on the Illumina 1.9 encoding using the American Standard Code for Information Interchange (ASCII) values of 2 to 40 followed by removal of the reads that have a minimum average Phred score of 10.
Accordingly, the data were filtered using the following criteria: minimum average quality score: 35 for a windows of 50, number of differences to the primer sequence = 0, maximum number of differences to the barcode sequence = 0, number of ambiguous base calls = 0, maximium homopolymer length = 8.
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