Spades-day2-pc.rar -

Inside your output directory (likely specified in your workshop instructions), you will find two main results: contigs.fasta and scaffolds.fasta .

It reduces the number of mismatches and short indels (insertions/deletions) by running a post-processing tool called MismatchCorrector. SPADES-Day2-pc.rar

Set a limit in gigabytes (e.g., -m 8 for 8GB). Inside your output directory (likely specified in your

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. conda activate micro612 ).

Match this to your CPU's physical cores to speed up the process (e.g., -t 4 ). 3. Focus on Scaffolds vs. Contigs

Activating the specific environment (e.g., conda activate micro612 ).