How is scaffolds.reduced.fa created?

[okokookk]

I ran redundans.py using the options --noscaffolding and --nogapclosing.
Below is the full run command I used.

python redundans.py --noscaffolding --nogapclosing -t 64 -f draft.contig.fa --identity 0.90 --overlap 0.95 --log draft.contig.log -o draft.contig

I used --noscaffolding, but not only contigs.reduced.fa, but scaffolds.reduced.fa was also written as output.
I did not use paired-end reads as input. What is the criteria that scaffolds.reduced.fa is output?
What is the difference between contigs.reduced.fa and scaffolds.reduced.fa?

[lpryszcz]

Hi, scaffolds.reduced.fa is the product of reduction of second to last step of the pipeline. Normally it's scaffolded and gap closed assembly (scaffolds.filled.fa), but in your case it's reduced contigs contigs.reduced.fa, since you run --noscaffolding --nogapclosing. Note, it's created even if there was no scaffolding.

What is the difference between contigs.reduced.fa and scaffolds.reduced.fa?

Simply scaffolds.reduced.fa in your case is result of two iteration of reduction.