Polishing with racon using multiple input files?

[BioLaFu]

Hi,
I have got a reference genome which I want to polish with more than just one sequence file.
Basically I've got a reference genome which was generated using PacBio and then I've got 50 whole genome sequences which were generated using Illumina.
Now I want to polish the PacBio reference genome using the "Illumina data". I managed to polish the reference genome once, with just one Illumina data set. But when I go ahead and try to polish the resulting file with the next Illumina data set I get the following error:
[racon::Window::add_layer] error: layer begin and end positions are invalid!

Is there a way to do what I want or is it simply not possible using racon?

I also thought about combining all of the Illumina sequences into one file, but that doesn't seem sensible, regarding I am working on snail genomes each about 1 Gb big....

Thanks in advance!
Laura

[rvaser]

Hello Laura,
unfortunately current API does not allow multiple files. You would need to combine them together and run Racon in one command. Also, if you have paired-ends they need to have unique names up to the first white space (you can preprocess the file before mapping with https://github.com/lbcb-sci/racon/blob/master/scripts/racon_preprocess.py).

Best regards,
Robert

[BioLaFu]

Hello Robert,

Thanks so much for your reply!
I am aware of the preprocessing step to get unique names for paired end data.
So I will go ahead and try to combine several fastq files into one, preprocess that and then run racon as usual...
Thanks again for your help.
Laura