If you are following a standard microbial genomics curriculum, your "Day 2" workflow typically involves:
Inside your output directory (likely specified in your workshop instructions), you will find two main results: contigs.fasta and scaffolds.fasta . SPADES-Day2-pc.rar
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 If you are following a standard microbial genomics