Module for Paired-End Sequences

Paired end sequencing is a common technique used in NGS. It produces two reads from proximal locations of a target DNA or RNA molecule in both forward and reverse direction,which could be potentially utilized to enhance the alignment precise and coverage.  Here, We present a method applying toRAPSearch2 that combine paired-end reads as one hit and evaluate the significance in the similarity search to improve sensitivity of alignment.

Based on the RAPSearch2 algorithm, we built a new module that could process the paired-end reads simultaneously. By using the paired end sequences aligned on the proximal locations on the same subject sequences, the method could increase the searching sensitivity by about 0.5%~0.6%, comparing to the similarity search by using each of the paired end sequences individually.
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