Aligning mate-less reads from a paired end read

[chsfredrick]

I've been trimming paired reads with DynamicTrim based on phred scores and using LengthSort to separate out those under 15 bases. LengthSort separates them into 4 files: 2 for the good reads, one for those under 15 bases, and one for the mates of the reads that were under 15 bases (but which are themselves fine). Is there any way I can still use the reads who were unfortunate enough to have a <15 base mate, or are they complete junk since they no longer have a mate? I am currently using bwa for alignment

[chsfredrick]

Alternatively, is there an aligner that will take a command to ignore reads under a certain length, thus not using those under a certain length but still using their mate?