Single-End mode for polishing with illumina short reads

[gitcruz]

Hi,

I have illumina data from HiC experiments, as often they come from distant parts of the genome, I would like NextPolisher to consider them Single End reads (avoiding any insert size inference). Is this possible?

Would this work by simply passing the fastq as separate files instead of the expected interleaved fastq for paired-end?

cat illumina.fofn will show: sampleA-R1.fastq.gz sampleA-R2.fastq.gz

Thanks, Fernando

[gitcruz]

I've just realized that among sge_option figures --unpaired. I think this should work and you can close the issue.

F.