using pair-end reads

[manuelsmendoza]

Does jabba work with illumina pair-end reads to correct the pb long-reads?

[gmiclotte]

You can use paired-end reads to correct long reads with jabba, but it does not use the paired-end information. In the jabba workflow the illumina reads are used to build a de Bruijn graph. Of course, you can clean up the de Bruijn graph with any tool that uses the paired-end information, prior to running jabba, but this is not the default pipeline.