Always prioritize scaffolds.fasta for your "Day 2" analysis. Scaffolds use paired-end read information to bridge gaps between contigs, providing a more complete picture of the genome. Common Workshop Workflow for Day 2
It reduces the number of mismatches and short indels (insertions/deletions) by running a post-processing tool called MismatchCorrector. SPADES-Day2-pc.rar
Match this to your CPU's physical cores to speed up the process (e.g., -t 4 ). 3. Focus on Scaffolds vs. Contigs Always prioritize scaffolds