Tools to identify read pairs?

[Kennels]

Hi,

After quality filtering reads 1 and 2 of paired end reads, the pairing information is lost.
I've been using the findpairs.py utility from the SHRiMP package to re-identify paired reads, but it requires large memory for large files, requiring one to split the files up. It works fine, but can anyone suggest other such tools?

Thanks

[Kennels]

I found this thread which implements a custom script and talks about others to do this job (with limitations):

http://seqanswers.com/forums/showthread.php?t=10392

If there are other tools please let me know, thanks!