Polishing long reads with illumina short PE reads.

[joao1980]

Hi,
I am fairly new to polishing methods so my apologies in advance for the basic question.
I have an assembly from long reads. I would like to use paired end reads to polish the assembly.
The repo states the following:
"Racon takes as input only three files: contigs in FASTA/FASTQ format, reads in FASTA/FASTQ format and overlaps/alignments between the reads and the contigs in MHAP/PAF/SAM format. Output is a set of polished contigs in FASTA format printed to stdout. "

So my question is:
Contigs = long read assembly file?
reads = merged PE short reads?
overlaps = alignment of short PE to the long read assembly file?

Thanks once again.
Cheers!
Joao