Transposons and Pacbio
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The advantage of PacBio reads is that they are quite long, so it may be possible to use methods designed for finding TEs in assemblies. I tested a workflow based on this protocol with Arabidopsis data and it worked quite well.
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nterhoeven
corrected with prooveread :-)
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nterhoeven
Yes, I know. Read the second sentence of my answer ;-)
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Ram
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What are you trying to do exactly? Map to a genome or infer repeat abundance straight from the reads? You are correct though, Pacbio is not as pervasive and most tools have been developed with Illumina or 454 data.
I was planning to do de novo assembly, and infer repeats from the reads
I would not normally try to assemble the reads, though this may be a reasonable approach with this data (depending on the species). Try Transposome, it works very well with long single-end 454 reads so I'm sure it will do fine with Pacbio. I'm the author of that tool so you can ask me any questions about it if you like.