use proovread to correct Pacbio reads with Illumina reads

Question

[shuchen]

I am trying to use proovread to correct Pacbio reads with Illumina reads. However, this process costs a very long running time. Is there any way to accelerate this process? I am thinking to normalize the read depth to 30X. Will this significanlt shoreten the running time? Hope there is someone had experience with proovread and your suggestion is very much appreciated.

Answer 1

[shuchen]

Also,when I designated multiple illumina fastq files, it seems that proovread only use the first fastq file for the correction. Do I need to merge all the fastq files before running proovread? Or I am not using proovread right?