sivico26 commented on May 20:
The command line I used to run Ra was the following:
ra -t $threads -x ont $ont_reads reads/ngs.fastq.gz > assembly.fasta
where $threads was set to 24 and $ont_reads, was the path to ont-reads and ngs.fastq.gz are Illumina reads.

BUT it is not clear WHAT is ngs.fastq.gz file? Paired-end raw reads?

My question is how to use Illumina paired-end raw reads?

I am going to use Illumina paired-end raw reads (DRR_1.fastq DRR_2.fastq) to polish my scaffolds.
Is this command correct?
ra -t $threads -x ont ont_reads.fastq DRR_1.fastq DRR_2.fastq > assembly.fasta`