Correcting PacBio with a hybrid approximation

[JaimeJR]

Hello everyone,

I have PacBio data and I would like to correct them with Illumina HiSeq short reads. I test several programs and finally decide to use proovread.

does anyone use this tool?

I chunck/split my data into 50Mb size files and proovread works fine with one file, but I have almost 500 files and work one by one is gonna take forever because I run proovread each time file by file.

proovread took the most time to processing the Illumina data and then correct PacBio sequences, does anyone know if you could run the program for more than one PacBio files in the same run?? I mean, if any chance to reuse the "temporary files" from Illumina and make the process faster and usable.

Thanks

[Bukowski]

Crossposted to BioStars: https://www.biostars.org/p/171829/

[rhall]

What is the goal of the project? Genome assembly? How much PacBio data do you have?
Correcting lots of PacBio data with short reads is very inefficient it may make more sense to redesign the analysis.