AFIK, Short sequencing and short pairwise sequencing generated by next-generation-sequencing is common now-a-days and there exists several alignment tools for them.

But I want to ask about long pairwise sequencing. There exists some alignment tools for long sequences like [rHAT][1]. That means there is at least one tool which generates long reads.

Now, I am asking that is there any tool which generates **Long Pairwise Reads**? if yes, then is there exist any aligner or mapper for that? Give me some idea about it.

Thanks in advance.


  [1]: https://github.com/derekguan/rHAT
Depends on your definition of "long". The idea of paired end sequencing originally arose with clone based sanger sequencing when sequencing primers would be designed to read in from both ends of the insert. This was used with short inserts (such as a standard plasmid based cloning vector) to a) effectively extend the maximum read length, OR provide two readings of a sequence for error checking. With long insert libraries, such as BACs, paired-end sequencing allowed placement of sequence on scaffolds, and detection of structural rearrangements and copy number alterations. 