Spades-day2-pc.rar -

Running the spades.py command on the cleaned "Day 2" datasets.

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.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 SPADES-Day2-pc.rar

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 . Running the spades

The most useful feature you should leverage for this topic is the during assembly. 1. Enable the Careful Assembly Mode

Using tools like Trimmomatic to clean your raw data before assembly. Focus on Scaffolds vs

Set a limit in gigabytes (e.g., -m 8 for 8GB).