With NextGENe’s Paired End Merging functionality, you can merged paired end reads by elongating the paired reads to the point that there is overlap between the two reads. The paired reads can then be joined together to form one continuous, longer read.

The number of elongation cycles that is required depends on the read lengths and the library size. Each condensation cycle generally increase the average read length to 1.6 the original length for shorter (<=36 bp) reads and to 6 bases less than twice the original length for longer (>36 bp) reads. These values might be reduced with an average depth of coverage less than 30x. For 75 bp reads from a 200 bp library, for example, a single cycle of elongation results in the reads being elongated enough for the paired reads to overlap. For 35 bp reads from a 200 bp library, three cycles of elongation are needed. You should extend the reads until a significant portion of the paired reads (roughly 15% of the elongated read length) are expected to overlap.

The paired reads are merged only if the overlapping regions match between the reads. Errors resulting from sequencing chemistry, basecalling, or the initial assembly by elongation will not match with the paired read, so the pair would not be merged.