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Cock, Peter JA, Christopher J Fields, Naohisa Goto, Michael L Heuer, and
Peter M Rice. 2010. <span>“The Sanger FASTQ File Format for Sequences
with Quality Scores, and the Solexa/Illumina FASTQ Variants.”</span>
<em>Nucleic Acids Research</em> 38 (6): 176771.
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