Can Bowtie2 or BWA handle over-lapping paired ends well??

[JackieBadger]

Hi guys,

My question is, how well do Bowtie2/BWA handle paired-end data that may overlap i.e. there is no insert?
Are these programs expecting some sized insert?
I know that a large proportion of our nextera data set comprises paired end reads that overlap, and from these I can build a contig based on shared similarity. Some paired ends do not overlap.
So can I treat the whole data set (with no prior contig building) as paired-ends and Bowtie2 would be able to handle and insert size that ranges from 0-100s bases?
I would think it wouldn't be an issue but I seem to remember someone mentioning they do not perform well without an insert between PE reads ....?

Thanks

J