The most useful feature you should leverage for this topic is the during assembly. 1. Enable the Careful Assembly Mode
SPAdes is known for being extremely memory-intensive. A useful practice during "Day 2" exercises is explicitly limiting its resource usage to prevent your PC from crashing. 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 The most useful feature you should leverage for
Running the spades.py command on the cleaned "Day 2" datasets. A useful practice during "Day 2" exercises is
Inside your output directory (likely specified in your workshop instructions), you will find two main results: contigs.fasta and scaffolds.fasta .
Using tools like Trimmomatic to clean your raw data before assembly.
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