COPE (Connecting Overlapped Pair-End reads) is a method to align and connect the illumina sequenced Pair-End reads of which the insert size is smaller than the sum of the two read length.The connected reads can be used in genome assembly, resequencing and transcriptome research.
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Bioinformatics. 2012 Nov 15;28(22):2870-4. doi: 10.1093/bioinformatics/bts563. Epub 2012 Oct 8.
COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly.
Liu B, Yuan J, Yiu SM, Li Z, Xie Y, Chen Y, Shi Y, Zhang H, Li Y, Lam TW, Luo R.