If works with long reads?

[CWYuan08]

Hi, we have some long reads that we don't want to build assemblies, and we are wondering if dnaPipeTE will work with Nanopore reads? Many thanks!

[clemgoub]

Hello!

dnaPipeTE is not designed to use long reads by default. However, I have once used it after chopping the long reads into 100-150bp bits. Though it is important to keep in mind that ONT reads will have a higher error rate than traditional Illumina reads, and thus the observed divergence between reads and consensus may be artificially inflated. However, I think it can still inform you about the general TE content and diversity in your samples.

Best,

Clément