AGILE is a sequence mapping tool specifically designed to map the longer reads (read length > 200) to a given reference genome. Currently it works for 454 reads, but efforts are being made to make it suitable to work for all sequencers, which produce longer reads. Looking at the current trend of increasing read lengths, soon most of the sequencers have read lengths > 200.
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Bioinformatics. 2011 Jan 15;27(2):189-95. Epub 2010 Nov 18.
Anatomy of a hash-based long read sequence mapping algorithm for next generation DNA sequencing.
Misra S, Agrawal A, Liao WK, Choudhary A.