Just I want to know what are the differences between the two outputs files, scaffolds.fasta and contigs.fasta in the assembler spades.py.
The manual don't provide any useful information at all. Please I don't want the definition of a conting or a scaffold, what I trying to understand is the technical part behind the spades algorithm, for example maybe spades.py is assuming that I am using any Illumina 1.9 sequencing machine but that's not enough information to determine the scaffolds or is it? How a scaffold is determined in the De Bruijn graph versus a conting? How spades.py knows the insert size of the specific protocol used to sequence, or just assumes one?
Help I am a little lost.
Any information will be useful.
Here is the manual's link http://spades.bioinf.spbau.ru/release3.6.2/manual.html#sec3.5