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Old 09-28-2017, 09:42 AM   #4
Brian Bushnell
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Location: Walnut Creek, CA

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Also, it's worth noting that Illumina base quality is reduced with each successive cycle due to phasing drift. This phasing drift is reset when a new read begins starting at a primer location. Therefore, reading the indexes independently, starting with their own primers, allows the index bases to be read without adding error to (or reducing the length of) the genomic bases.
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