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We cluster flowgrams rather than reads and operate solely in flow space (see Section 1.2).
However, this problem has been resolved by the use of the de Bruijn graph which models overlapping sequences rather than reads, thereby reducing the complexity of dealing with multiple reads [ 25- 27].
HTSeq provides a function, pair_SAM_alignments_with_buffer, to pair up these records by keeping a buffer of reads whose mate has not yet been found, and so facilitates processing data on the level of sequenced fragments rather than reads.
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