Transposons and Pacbio

Question

[burnsro]

What tools are available to call TEs using Pacbio data? My understanding is that most work using paired-end reads from short read Illumina data.

[SES]

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.

[burnsro]

I was planning to do de novo assembly, and infer repeats from the reads

[SES]

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.

Answer 1

[nterhoeven]

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.

[thackl]

Did you use raw or corrected PacBio reads?

[nterhoeven]

corrected with prooveread :-)

[SES]

That protocol is for identifying repeats in a genome assembly. OP wants to infer repeats from the reads.

[nterhoeven]

Yes, I know. Read the second sentence of my answer ;-)